SGA: The Great Tau'ri War Pt 3: Vengeance
by Ariston-1
Summary: In 2045, Thirty years after the end of the Great Tau'ri War, two former Atlantis crew discuss the final days of the war, the death of so many close to the them, how it effected them and how a dark secret changed the fate of the galaxy forever. (this will darker the the others, & answer some questions I have created from parts 1 & 2)
1. Chapter 1

_**Stargate Atlantis:**_

_**The Great Tau'ri War**_

_**Vengeance**_

The Great Tau'ri War, a conflict that tore apart the Milky Way Galaxy had ended almost 30 years earlier, like a Phoenix from the flames the Tau'ri of Earth arose to a great power within the Galaxy. After re-establishing contact with the Pegasus Galaxy and Contact with another, the sphere of influence had spread to become perhaps the first true Trans-Galactic Empire ever created with the Ancient City of Atlantis at the centre of the vast empire with in '_The Three Galaxies_'

**In 2045...**

Once the base of operations for the war against the Wraith and the deadly Lucian Alliance, a tired aging General stood in the centre of the Command Centre of the city awaiting the arrival of the President of the Tau'ri, a pivotal cog in the ever-expanding Empire that spanned many races. Once a proud warrior, now more of a figurehead assigned to command the Capital of the Tau'ri Alliance.

"Off world activation… receiving IDC. It's the President"

Standing tall the old warrior straightened his tunic as he awaited the President's party too arrive from their good will tour of the Pegasus Galaxy, since the Wraith had become extinct, the Tau'ri had picked up the pieces within the Dwarf Galaxy and made it a second and vital piece of the growing empire. Finally, after waiting the President's personnel guard began too appear through the Stargate as the old General smiled and stepped forward.

"Mister President, welcome home"

"Thank you General"

"How was the tour?"

Smiling slightly the President placed his hand on the shoulder of his old friend as he shook his hand.

"Awful…" The President laughed.

"Then next time, perhaps I should show you a little place I… Forget it"

"Of course, so how are things? Miss me much?"

Laughing slightly the balding old General placed his arm around the shoulder of his old friend s he led him up the steps towards the command centre, slowly the President's eyes fell upon a single console as the General nodded slightly.

"Miss it, don't you?"

"A little… but that is the past. So what's happened here? Anything amazing?"

"No, the Jaffa have built another ship, that's it really"

"Great!" The President mocked.

"Well at least you are back in time for the memorial service"

Closing his eyes, he cursed himself slightly as he muttered.

"I thought that was last week"

"Nope, tomorrow… You're speech is already penned for you. Ohh, by the way… some one is waiting for you in your office"

"Who?" He sighed.

"I promised it would be a surprise"

Mustering up the energy to nod, the President turned and left the control room. As he reached the exit, he turned and looked at his old friend.

"Thanks Ronan, dinner later, Karen and the kids have been asking about you?"

"Of course… Mister President" He smiled.

Finally the President reached his office, it had always been difficult since he been confined to walking with a cane but it was something he had gotten used to over the years, slowly shuffling into the office he sat down in his chair as a voice called out from the darkness.

"Well, you're the last person I expected to see in _THAT_ chair"

A large smile crept over his face as a figure stepped into the light; almost laughing slightly he tried to stand as a hand motioned for him to stay seated.

"How the hell did you get here? I thought you where on Chulak"

"Well, you know me… I can't stay away from this place"

Laughing the President motioned for the figure to sit down as he reached into his desk and poured out two drinks of whiskey.

"Mister President, you know that is illegal now"

"I make the rules around here… besides… Karen is off world. You know what they say… what she doesn't know…"

"You've done well for yourself. The first President to take three terms in office"

"I know…" He said with a smirk.

Accepting the drink the guest of the President sat in a chair facing him as the President took a sip from his glass.

"Well, I see the years haven't been kind to Ronan"

Laughing slightly the President placed his drink on his desk and leaned forward as he spoke.

"It's good to see you again John, you look good"

"Thanks Rodney… or should I say Mister President?" He laughed.

"You know what? Screw the titles… I haven't seen you in years. Here for the memorial?"

"Memorial?" He sighed.

"Yeah… thirty years since the end of the war. Thirty years since… yeah! How are you doing John?"

"You know me McKay…" He mumbled.

"Yes, I do. That is why I asked… a lot of us have been talking about the past John…"

Shifting uncomfortably in his chair, the former General leaned forwards as he spoke.

"About what McKay?"

"You, we've been worried about you John. It's been thirty years since…"

"Since Cole disappeared… yes I know. I'm over that"

"Yes I know, three failed marriages. Discharged from service… should I go on?"

"No…" He mumbled.

Slowly the former General leaned forwards and took a sip of his drink, as he seemed to gaze off into the distance.

"John, I heard about the diagnosis… how long?"

"I thought you might, two years tops…"

"That was two years ago" McKay said with concern.

"Surprise!" Sheppard mocked. "You know… I was thinking a few days ago about…" Laughing slightly "… You know"

"Ohh that. You know I still have the Airplane"

"Really?" He smiled.

"Yeah, it's in a hanger on the main land" Rodney Said with a smile.

"I can't believe what it really took to get Cole to return, I always thought she would have jumped at the chance to get even"

**In 2015...**

The winter wind blew threw everything as it ripped around the barren land, no crops could survive at this time of year, yet it was the perfect time for working on the side project that had taken up most of her time. Music blared out in the old converted barn as worked oblivious of the noise from outside.

Slowly and carefully, the new design of Tau'ri built Jumper based on the Hybrid touched down on the soil as facing the old farm as a man exited the nearest building holding a large double barrel shotgun.

"_GET THAT DAMNED THING OFF MY LAWN!_" He yelled as he approached.

Slowly Ronan placed his hand on the weapon at his side as he exited the craft, concentrating on the moment he raised his left hand as he approached the elderly man side on hiding his right hand that was unbuckling the clip that held his particle weapon in place.

"Easy sir, take it easy. Put down the shotgun"

Cautiously General Sheppard exited the craft as the metal cane clicked on the ramp while he pulled his jacket around himself and stepped onto the soil, smiling slightly he stepped between Ronan and the old man as spoke over the howling winds.

"I'm Major General Sheppard. Please lower your weapon sir…"

"Sheppard? John Sheppard, from Atlantis?" He yelled.

"Yes sir… This is Colonel Ronan Dex and the guy behind me is Lieutenant Colonel Rodney McKay. Sir it's freezing out here, can we step inside?"

Lowering his weapon to the ground he waved them on as he stepped into the old barn house, smiling slightly Sheppard and his old friends followed the old man into the house as a car arrived at the door. After receiving a package from the courier, the old man stepped into the house and closed the door behind him as snow began to fall.

"Well, to what do I owe the pleasure General?"

Slowly the old man placed the large package on a table before him as he lead the Atlantis personnel into a large room off to the left of the main living area. Sheppard stopped for a moment as he looked around in awe at what he saw.

"Since the beginning of military aviation, my family have been military pilot's sir. Every generation of my family are represented on these walls by their awards and medals"

"Impressive sir…" Sheppard said with respect.

"I've heard a lot about you General. My daughter speaks very highly of you all"

"Is she here?" Ronan asked politely.

"That depends on what you want, her resignation was sent to the President a few weeks ago. If you have her discharge papers then yes. But I doubt they would send you sir"

Slowly McKay walked the length of the room as he looked at each medal and commendation in sequence until he stopped at the last, his jaw dropped as he took in the impressive collection before him.

"Ohh my god. Congressional Medal of Honour, Distinguished Flying Cross, Two Purple Hearts and the Silver Star… to name but a few. You must be very proud sir"

"Those are not mine" He laughed. "I was an Airforce Captain… I take it you missed the Navy Cross?"

"These are you daughters?"

Slowly Sheppard walked towards the display as his jaw dropped by what he saw, a collection of some of the United States Military's highest medals and commendations hung on the wall before him, quickly his head whipped around as he looked in shock at the old man.

"I've seen your daughter in her dress uniform sir; she does not wear these ribbons"

"Jenny believes that a person's career is not defined by awards… but by one's actions. She sends them home for display on this wall as a private memorial"

"Wow, I had no idea"

Laughing slightly the old man turned and exited the room as they stood gazing at the large collection before them, finally he returned with the large box and handed it too Ronan with a slight salute as he spoke.

"Well gentlemen, if you wish to speak with my daughter, you should bring this with you. She's in the old barn outback"

"Thank you sir" McKay smiled.

"Well, which way sir?" Sheppard replied with a salute.

Smiling he led them out of the large room, threw the kitchen and out of the house. Pulling his jacket around himself, he pointed to the old barn as the three left the main house and finally pulled open the door to the large barn. As they stepped inside Sheppard's jaw once again dropped as he came face to face with an old legendary world war two aircraft. Smiling slightly he ran his left hand over the tail of the aircraft as the music blared out in through the old barn, quickly McKay found an old radio and switched it off as the sound of a metal wrench falling caught their attention.

"Dad, what the hell are you doing?" A voice yelled out.

Slowly from the front of the aircraft a dirty oil covered figure appeared ducked out from under the large metal propeller and walked towards the radio and once again switched it back on with, sighing she looked up at Sheppard and Ronan and shook her head as she walked back to the front of the aircraft.

"_COLE… WE NEED TO TALK_" Sheppard yelled.

"_NOT INTERESTED SHEPPARD_"

Once again, McKay turned off the music as Cole walked towards him and laughed slightly.

"You screwed me over; I've already sent my resignation. I'm not returning to Atlantis John"

Smiling she looked at the package Ronan was holding and took it from him as she laughed.

"You're not the unusual Courier, but at least you can hold this without showing strain. Thank you Ronan"

"No one screwed you over Cole…" Sheppard yelled.

"Ohh Bull Shit! You had me committed Sheppard. Do you have any idea how long I spent in that hospital?" She barked as she stepped face to face with him.

"It was only two weeks Cole… I checked"

"Was that it?" She laughed. "It felt like a life time listening to those people howl at the moon"

Smiling slightly, she turned and walked back towards the front of the aircraft as they followed her, McKay ran his left hand down the fuselage of the cold metallic aircraft softly as he spoke.

"Supermarine Spitfire… a Mark V?"

"Mark Vb actually" She laughed.

"She's a beauty"

"She hasn't flown for forty years…" Lovingly she looked up at the aircraft. "… But that won't be long, right baby?"

"Cole… we found something"

"A conscience maybe? Congratulations Sheppard"

"Funny" He replied. "Someone had placed something outside your quarters, just below the window, McKay?"

"Cole… the device was designed to access your subconscious mind… we believe it was designed to send those images into your mind…"

"Sounds a little Star Trek-ish to me. Look, why are you here… now?"

"We've found the Clone…" Ronan replied.

"I'm happy for you"

"After the attack on Earth and loosing half his fleet for nothing, the Lucian Alliance turned its back on him. However, he still controls a large fleet, he's currently attempting to take on the Lucian Alliance… but his position is weak. We believe that a full assault on his command centre will…"

"Will what? Ohh I get it, you want me to lead that attack? Piss Off!"

Carefully she opened the package and smiled slightly as she looked inside, the last vital component of the powerful of the Rolls-Royce Merlin engine lay before her, smiling she reached into the box and pulled out the final piece as McKay looked on with a smile.

"Reproduction?" He asked.

"What,? Are you crazy? Every piece of this aircraft is original right down to the rubber in the tires. I've been working on this baby since I was a kid. My grandfather taught me and brother how to fly in an old bi-plane when we where kids… I got my pilot's licence before I could drive. This beauty was his dream…"

"That's great Cole, okay… don't do it for me… or the thousands that died last year… do it for yourself. Come with us"

Laughing she looked up at the roof as she replied.

"Give me one good reason why?"

"Revenge?" Ronan said with a dark smile.

A slight spark appeared in her eye as she turned to look at Ronan, the thought of revenge against the one who had destroyed her life was a good reason; however, the fact that everyone she had trusted over the past years had turned their backs on her had cut her deep. Breathing deeply she removed the rag tied around her hair as she stepped closer to the three officers.

"Revenge is always a good reason Ronan; you know that better then anyone. But I can't…" Smiling slightly she stepped in front of Sheppard. "As you can see, I have a lot of work to do here. I'm sorry sir…"

Nodding slightly Sheppard looked at his two companions; slowly he turned to leave as Cole took his arm and looked up into his eyes.

"It's good to see you again John, you look good. How's the leg?"

"Hurts in the cold" He smiled.

"Well, it's snowing outside. You'd better get warm. Ronan, take care of him"

Smiling slightly she ran her hand down his arm and winked slightly she turned back to the large aircraft before her, as she walked away she stopped slightly as McKay stepped too her side.

"What?"

"If you need any help with this, call me. I'd love to get my hands on this engine"

"I bet you would…" She laughed. "… Well, so long Major"

"Actually, Lieutenant Colonel now"

Slowly she leaned towards him and kissed his cheek as she whispered.

"Happy for you…"

Blushing slightly, McKay stepped back as he coughed and flashed a ring on his left hand.

"Engaged? Congratulations… Who is it?"

"Karen Wilson, she's the new Chief Medic"

"New? What happened to Beckett?"

"He took a job working as the President's personal physician. You look good Cole, although I did prefer you as a red-head"

Laughing slightly she ran her oil covered fingers threw her dirty hair as she blushed slightly and replied.

"Original colour, I thought I'd give the blonde Jennifer Cole another try. Take care of each other guys; it's good to see you again"

Saluting the three once more she returned to her work as McKay rejoined Sheppard and Ronan as they left.

Once back inside the jumper McKay sat in the pilot's seat as Ronan sat behind while Sheppard sat in the co-pilot's seat next to him with a dark smile on his face.

"She won't return" Ronan said.

"Ohh… she will"

"Care to bet?" McKay said to Sheppard.

"Alright, if she isn't back within say… one week, you guys take a month off anyplace you want"

"Deal" They both said in unison.

Smiling too himself Sheppard sat back in his seat as the jumper lifted off and disappeared into the snow covered sky.

Sighing too herself Cole threw down the large wrench she was holding and looked up at the ceiling as footsteps walked towards her.

"What is it dad?"

"I take it from the look in your eyes that you are staying?"

"I have work to do dad" She mumbled.

"Yes, you do… I remember you telling me about Sheppard; it was something more then talking about a superior officer…"

"Say it" She barked.

"You have feelings for him, don't you?"

All she could do was laugh to hide her tears as she turned towards her father and spoke through her deep feelings.

"Once yes maybe…"

"You might be able to lie to them young lady, but not to me. They came all this way just to ask you to go back with them. What is it you really want Jennifer?"

"I-I don't know"

"I see listen, the reason I'm here… I just got a call from the hospital, it's time"

Her legs buckled as she wept freely, slowly he knelt down next too her as his knees cracked and creaked she wrapped her arms around him for comfort almost as she had done as a child.

"We should go, your Grandfather has been asking for you"

"Let me clean up first"

"Of course, he asked one thing of you first"

Laughing past her tears she looked up and nodded, she knew exactly what he meant; her grandfather had always been impressed by his granddaughter in her military dress uniform and wearing her full collection of medals.

"Of course dad… give me an hour"

"Take what time you need Jennifer"


	2. Chapter 2

**In 2015... **

**December 21**

A sombre feeling stayed with the two as they exited the old Ford pick-up truck and slowly walked into the house, placing her bag on the table in the main living area former Colonel Cole sat in an old small chair as her tears began to flow free. Slowly her father crouched next to her and attempted to comfort her with a soft and soothing voice.

"He was 92 Jenny, he had a good life"

"I know dad, but it still hurts" He sobbed.

"He was a good man. You should be proud of what he had accomplished"

Smiling she looked up and laughed slightly.

"I am, I always have been… it's tough dad… Grandma, Bobby, Mom and now Grandpa…"

"I know… it never gets any easier loosing the ones we love"

"What now dad, what do we do now?"

"Remember him, what he did… what he meant to you and carry that with you forever"

Slowly the old war veteran chocked back his own feelings as he stood and poured two drinks from an old bottle of Scotch Whisky as he spoke past his own grief.

"Grandpa bought this the day you where born, he said you would change the world one day…"

"Well that worked… San Francisco was almost destroyed by…"

"Not you Jenny, not you. Here drink with an old man?"

Wiping her tears away she looked up and took the glass and drained it quickly.

"Wow!" She coughed.

"Wow… indeed. Another?" He coughed.

"No… I should get back to what I was doing"

"You can't leave that thing alone can you?"

"No sir, now more then ever…"

"What did he mean when he said '… _The meal was cooked long ago…_'?"

"I don't know, he was dosed up on medication dad"

Smiling slightly she placed her glass in her father's hands as she walked past him. Changing quickly she braved the snow storm and entered the old barn as she looked over an old schematic of the aircraft she had almost completed, placing the book down she turned on the music once again and picked up the final piece of the engine she had been awaiting for weeks, as she turned around she dropped the valuable engine part and ran into the centre of the barn looking around in shock.

"_BASTARDS…_You total bastards"

Screaming with everything she had she ripped the old radio off the counter and threw it across the room as she kicked open the doors and walked towards the main house. Her first thought was one of pure anger until she entered the living area of the house and saw her father with his head in his hands crying, wiping back her own tears she quietly walked backwards into the next room and grabbed the first weapon she could find, her grandfather's service pistol. Holding it close too her chest she mumbled too herself quietly before leaving the house.

**In 2045...**

Taking another sip of his drink President McKay smiled as his memories began to flow back of that time, a time when the Great Tau'ri War was at it's height and danger hid around every corner as the enemies of Earth had begun to mobilise against them.

"… I mean, I'm surprised John"

"At what Rodney?" He said as he took another sip.

"That she didn't kill you"

"Yeah, me too" He laughed.

"You know, I thought a lot about those years recently. You know that Cole reminded me a lot of Teyla"

John almost chocked on his drink as he laughed slightly, although he similarity was clear after he had said it.

"Are you kidding me?"

"No, imagine what it would have been like if they had been around together"

"Rodney, that's the single stupidest thing I have ever heard"

Laughing Rodney leaned forward and refilled the drinks as John leaned forward and began coughing uncontrollably. After a few moments he wiped the blood from his mouth and took a sip of his drink as Rodney looked on in shock and concern for his old commanding officer and friend.

"Are you okay John?"

"I'm fine… it happens, now where was I? Teyla and Cole. You know they would've hated each other, from day one"

"One side of the same coin"

"They would have… beaten the shit out of each other and then fought over who won"

"Wow, Rodney McKay… the most influential President in Tau'ri history… using a swear word. Tut, tut, tut… what would you wife… and voters think?" He laughed.

"Lucky for us, they aren't here. So come on, tell me the truth… how did you get Cole to come back?"

"Well that was the tough part…"

"I remember when she… beamed in, holding that old gun"

"What was the one thing she valued the most?" He smiled.

"Ohh you didn't…"

John took a sip of his drink as he smiled slightly.

**In 2015... **

**December 21**

For the first time since the great city had arrived on Earth Christmas decorations had been hung around the gate room of Atlantis as the festive spirit had taken over them. Since the cowardly attack on earth over a year ago, moral within the city had hit an all time low. Stood looking down over the control centre General Sheppard had a large smile on his face as he watched his command move around with a slight spring in their steps for the first time in almost a year as Doctor Zelenka walked towards him he turned and smiled slightly.

"Radek, what can I do for you?"

"Nothing sir… actually, a few of us have been wandering, why are you smiling all the time?"

"McKay caught his hand in a car door" He laughed.

"Although funny, it isn't that… what is it"

"Really, Not buying it? Okay…"

A beeping sound caught Zelenka's attention as Sheppard straightened his tunic and stood tall.

"Wait for it… three… two… one"

A bright flash of light appeared in the centre of the Gateroom as a dirty angry woman looked around and saw the both of them stood looking at her with a slight smile on their faces. Anger swelled as she walked pushed past several of the personnel only to be stopped on the first step by Ronan.

"Get out of my way Dex" She growled.

"I can't dot hat Cole, I'm sorry"

"_MOVE!_" She yelled.

"I'm sorry, hand over that gun"

"If you want this gun Dex, you're going to have to take it from me"

Slowly Ronan walked down a few steps as Sheppard looked on with a smile.

"I have the high ground Cole, you'll have to get past me"

"Not a problem…" She said with a smile. "… Just remember one thing Ronan, this isn't about you. And I'm sorry"

"For what?" He asked.

With almost lightening speed she grabbed him and threw him past her as she quickly spun around as he landed on the ground behind her and rolled before jumping too his feet, smiling slightly he ran his right hand over his lips as they began to circle each other, a large group had gathered around as Cole placed old service weapon inside her overalls as she began to asses her opponent's strengths and weaknesses, if he had any. Almost a clear foot taller then her he had the advantage of reach, but she had been highly trained in many different forms of self defence and rarely lost a sparring session against him in the past.

"Don't do this Cole…"

"Too late Dex, he's gone too damned far this time"

He had never seen this side of her as she used his own fighting style against him, quickly he dropped to the floor to avoid her powerful attack as she leapt into the air and slammed her fist down onto his nose as a crack was heard, falling to the floor he rolled as blood poured from his nose and upper lip, blood filled his mouth, wincing in pain slightly he spat the blood out of his mouth as anger began to swell to a dangerous level within him as he grabbed her and picked up in a powerful bear hug, resisting the urge to scream she ploughed both her elbows down onto his shoulders over and over until his grip was loosened enough for her break free, stepping back slightly she clenched her fists once more as she spun around and swept his legs from under him. As he fell she followed through with a powerful kick too his jaw. As he fell to the floor she grabbed the large energy pistol off his belt and quickly ran up the steps towards the General. Her eyes burned once more as se pushed past the guards and grabbed Sheppard by his tunic and threw him into the nearest console, the sound of Ronan's large pistol activating shocked everyone as she pushed it into the side of Sheppard's head and yelled with all of her anger.

"Where the hell is it?"

"You are this close to being Shit-canned Cole!" He grunted.

"I don't know much about this weapon you Bastard… but I know one thing, Stun or Kill setting, at this distance it will blow your damned head off. Where the hell is it?"

"Safe, for now"

Quickly he pushed back as she threw him down once more, from the side of her eye she saw two security guards slowly walk up towards her, without thinking she grabbed the old service pistol from inside her overalls and pointed it at the two guards as she pulled down on the hammer.

"I want it back Sheppard… _NOW!_"

Slowly he stood and pushed the weapon away from his head as he paced around her.

"You've lost it… You have no idea what the hell is going on do you? For over a year you've been sat around working on your little project while we're dying for your freedom. Put down those weapons Cole, and I won't have you arrested… hear me out, you owe me that much!"

From the corner of her eye she saw one of the two guards walk towards her, reflexes kicked in as she squeezed the trigger on the old service pistol, sparks flew as the bullet slammed into the floor at the guard's feet. Slowly Sheppard raised both his hands as he walked towards her and pushed the large particle weapon away as he spoke softly.

"We all know what happened to you Cole, and we could have all handled it better then we did… for that, I'm sorry. Jack set you up for the fall… we don't know why he did. I offer you a chance to get even with him, work with us again… help us stop him once and for all… help us end this war. Not for me, not for those thousands that died during the last attack but for yourself… Ronan was right Cole, revenge is a great motivator"

Slowly she lowered her weapons and placed them on the console next to her as grief and anger began to boil over. Collapsing to the ground she began to cry as Sheppard knelt down next too her and placed his hand on her back in an attempt to comfort her.

"Okay John, but after this I'm done… finished with it all. If I see so much as a scratch on the paint work on that plane… I'll kill you, do you understand me Sheppard… I will kill you"

"I got it Cole…" He laughed slightly. "Welcome back. Captain Forest, take the Colonel to the Infirmary, have her check out by the Doctor, once she's been cleared I want to see her in my office… we have a lot to talk about"

"Aye sir" He said slowly.

Nodding slowly she stood and turned to face the large man behind her, wiping her eyes she followed him out of the control room as Ronan stepped beside her with a smile on his face as blood poured from his broken nose and large cut on the side of his jaw.

"You're good Cole… But I want a rematch"

"Are you okay Ronan?" She said with concern.

"I'll live, this ain't my first broken bone. Welcome back"

With her head low she followed the two large men towards the infirmary as she spoke with a shaky voice as she attempted to hold back her own sense of personal loss.

"Do me a favour Dex?"

"Of course"

"Help me find Jack… 'Cause I'm gonna kill him. But first I'm gonna make him pay for everything he's done"

"I give you my word"

"Thank you… sorry about…"

"Forget it. I got one question though, it's bothered me for awhile now"

"What is it?" She asked quietly.

"You seem to know what people are going to do before they do it… how?"

Laughing slightly she stopped and looked up at the large alien soldier, since Atlantis had become stranded on Earth, he had made this planet his home almost to the point of adopting Tau'ri speech patterns.

"I don't know… I've always been able to do it, it's like I can almost sense an opponent's thoughts before they make the choice to act and mount the appropriate defence. That's how I've always been able…" Smiling at him she continued with a mocking tone. "… to beat you. You're a beast Dex, your skills and training are insane… so far beyond my own you scare me. You almost had me back there but you hesitated, you blinked… why?"

"I don't know… but thank you"

Laughing for the first time in over a year she followed the two towards the medical section of the large city, after being cleared for duty she returned too her old quarters and looked around, it almost looked the same as when she left it with the exception of a new Tau'ri Alliance uniform carefully placed on the bed. After taking a shower she changed clothes and walked towards the command centre as the shocked senior staff watched while she walked towards the General's office and entered.

"Not in wearing a uniform Cole?" Sheppard said with a smile.

"No sir, what I have planned for that Bastard clone… I do not want to be on the conscience of the military… or you"

"I see, civilian it is then. Take a seat, we have a lot to talk about"

"Aye sir" She said with respect.

"I took the liberty of contacting your father for you, to inform him that you have returned to Atlantis"

"I see" She grunted.

"He's worried about you Cole, he told me about your Grandfather… I'm sorry. The aircraft has been returned intact… I've also tracked down the final parts you need to complete the aircraft, they will be sent to your home as soon as possible"

"Thank you sir" She said with a smile.

Slowly he picked up a file and slid it across his desk towards her, as she opened the file she began to read the first page, a classified security file on the man now known as the Asguard designed clone of Jack O'Neill.

"That is everything we have on the clone, it's not much but we think we know why he turned against us"

"Why?" She said through gritted teeth.

"Shortly after he graduated from high school he joined the Marine Corps, with his knowledge he was fast tracked up the ladder at an amazing rate. However, he was discharged from service after almost killing his superior officer during a bar fight. After being kicked out of the Military and the death of the Asguard race he went into hiding… we don't know where he went but a few years later he was spotted working for a… small private army. He was arrested many times for smuggling weapons… we believe he was responsible for the attack on Atlantis that destroyed our Stardrive capabilities. The destruction of the Stardrive was a by product of his true intent"

"He wanted to kill General O'Neill?"

"We believe so… it was the perfect time to assassinate him and many of the leaders of the military that had gathered to inspect Atlantis"

"I see, where is he now?" She growled.

"His fleet moves around a lot however, a Jaffa vessel spotted his command ship here…"

Quickly he leaned over the table and pointed to a star map on his desk.

"… A small system on the edge of our galaxy. Unfortunately the system has no Stargate we are aware of so gating to the system is impossible…"

"I sense a… however coming Johnny Boy"

Laughing slightly he leaned back in his chair and nodded with a large grin on his face.

"We have a… new ship docked on the East Pier, top of the line… all the latest tech. It's a small ship, larger then an Al'kesh. But this thing is the fastest ship we have, it's weapons systems put a 304 to shame…"

"Nice!" She smiled darkly.

"It's the first ship designed with Asguard, Lantean and Tau'ri tech… Primary and Secondary Shield grid, Primary and Secondary cloaking shields… Think Defiant from Star Trek"

"Cool…"

"She's yours Cole… take the ship and anyone you need. Bring that bastard clone back"

"With no due respect John… once I'm finished with that asshole, there won't be much left to fit a match box"

"Be careful Cole… we think he's working on some kind of Ascension"

"Even better… one question, well two actually. What happened to his wife?"

"She gave birth to a boy, they're both in hiding. She gave us everything we have in that file in exchange for sanctuary on Earth and immunity from prosecution"

"Cowardly bitch. Give me Ronan and Zelenka…"

"Zelenka, why?" He laughed.

"Trust me… What's the name of the ship?"

"Vengeance" He replied as she smiled darkly once again. "I had a feeling you'd like that, By the way… She's equipped with two new support vessels, a new design fighter based on the 302"

"And the other?"

"The new Tau'ri Jumper you helped design…"

"Perfect!" She laughed.


	3. Chapter 3

**In 2045...**

Lunch had been served to the President and his honoured guest; a gourmet chef had prepared the meal especially for them, although most of the meals served throughout Atlantis where now protein resequenced President M. Rodney McKay preferred real food, especially since his many allergies had been corrected by the new advances in Medical Science. With a slight laugh, Sheppard looked down upon the meal before him as his old friend began to eagerly devour his meal.

"Rodney… Rodney, what is this?"

"Ohh Sorry…" After he swallowed his food. "Potato slices baked with a Chilli powder, Garlic, Black Pepper, Lemon and Lime garnish, actually my favourite and Piri-Piri Style Sausages. It's a little spicy, but you'll love it"

"Really? Sounds a little funky to me. But you only live once right?"

Throwing caution to the wind, he took a large bite of the meal before him. Smiling slightly at his first bite he begun to eat the large meal before him as they continued their conversation.

"…Anyway as I was saying. After she left my office I had to tell Zelenka he was recruited"

"I take it he wasn't happy with his new assignment?"

"The opposite actually, he loved the idea. The clone had screwed up so many systems on Atlantis he was the one who you decided had to fix them"

"Yeah… perks of being his department head" Rodney Laughed.

"She never told you this… as far as I know but Karen was a little pissed off that you didn't go, after all… you designed that ship"

"I know… she told me"

Smiling he looked down at his meal as he continued eating like a hungry man enjoying his first meal in days.

"This is… amazing"

"Isn't it?" He said with a smile. "Karen hates it; the kids love it… not as much as hotdogs of course. I gotta admit one thing though… I was surprised when I saw Cole on the ship though"

**In 2015... **

**December 21**

It had taken many years of intense research and development to create the advanced cruiser now docked in a secured hanger hidden away from view on Atlantis as the latest ship awaited its crew. With a large and dark grin on her face, former Colonel Cole stood before the vessel taking in the view of the ship. Its sleek lines had followed none of the traditional design features of the standard Tau'ri ships, the deepest black possible with no portholes or external lighting, only illuminated by the lighting from above and below. Smiling too herself she looked around as Ronan walked up too her side.

"What do you think Cole?"

"She'll do, how's the nose?"

"Broken, the doc was able to fix it"

"Sorry" She laughed.

"No, your not"

"You're right. Hey if I can beat you down…"

Smiling slightly Ronan his placed his hand on her shoulder as turned to look at her with a smile.

"I heard about your grandfather and mother… I'm sorry"

"Thanks Ronan. Mom went last year, Grandpa… was different, and he taught me everything I know"

"I understand, my grandfather taught me how to track and hunt when I was a child. You know John talked about you all the time"

"Really?" She replied with a smile.

"He hasn't been the same since you left. But now that you're back…"

"Hey wait a minute… I'm only here to take down that asshole Jack. Once that's done, I'm long gone Ronan"

Ronan walked towards the ramp leading to the interior of the vessel as he laughed slightly and replied.

"No you're not, you can't stay away Cole!"

Running after him she stopped in front him with a smile as she replied.

"Ohh you're so wrong, but thanks anyway"

"You'll stay, once you see this ship in action. You _WILL_ stay and take command"

The interior of the ship was nothing like the outside, sleek and smooth walls that had none of the design features of anything before it, even Atlantis its self appeared low tech compared to the interior. The smell of the new ship was almost intoxicating, a sweet odour of honey mixed with fragrances she had never experienced before covered the interior as she walked the halls towards the bridge of the new ship.

"What the hell is that amazing smell?"

"Ohh, we can't pin that down, it's driving McKay nuts"

"Leave it then" She laughed.

Stopping at a door, Ronan turned to face her with a slight look of mischief in his eyes as he spoke slowly.

"Are you ready?"

"For what?"

"The bridge, now remember this. It is not the ships you're used too… this thing is hopefully a new line. No one has designed a ship like this before, these controls are new and state of the art. Very few pilots can handle this ship… she's fast and powerful"

"What are you hiding Dex… I'm ready"

"Alright… listen a few weeks ago I took her out for a little ride around this system… the damned thing is smooth Cole, very smooth"

Laughing slightly she attempted to push past him as he placed his hand over the only door into the bridge she could see.

"Remember one thing Cole… this ship will punish you if you handle her wrong. It did with me, I almost crashed her"

"Into what?"

"Jupiter"

Laughing she placed her head on his chest as tears began to flow; finally she looked up and replied.

"The largest planet in the damned system and you almost hit it?"

Rubbing the back of his neck, he laughed slightly as he looked down upon her and replied.

"Yes… you'll see. Ready?"

Standing before the door before him a sound of a hum followed as the door opened, entering first Ronan stepped too his left as Cole followed and stopped, her jaw almost hit the floor as she looked around slowly.

"Holy F…"

"Yeah!" He said quickly.

The bridge of the vessel was a large oval shaped with consoles lining each walls, at the front of the vessel was a blanked out wall that followed the curve of the design. Each station followed the smooth shape of the vessel yet emulated the design of the corridors she had walked through. Slowly she entered as she ran her fingers through her hair and laughed to herself.

"What do you think?"

"What do I think?" She laughed. "What the hell is this, the Enterprise?"

Holographic displays lined the walls as they appeared to float free of the consoles below, each one displayed a unique reading in English. Smiling too herself she was almost afraid to step onto the bridge. Laughing slightly Ronan took her arm and led her towards the nearest console as he spoke.

"This is the ship's status display… with limited space each console has the potential to become any display called upon. Following the flow of the design is engineering and transporter control, environmental control, backup station one, the main screen which is holographic, back up stations two and three, weapons stations which control defensive and offensive systems, communications and science station and on the back wall is ship's status with a schematic of the vessel for damage control and other key systems. The command chair with slave controls to all prime systems including weapons stores and finally the helm of the ship, which includes navigation and other key systems"

"She'll do. What kind of weapons are you taking about, Asguard beams?"

"Not exactly, I don't understand it myself… but some one around here will let you know about them" He replied with a large smile.

"Of course…" She smiled. "Well, get who ever is in charge of construction up here, I want to be able to launch as soon as possible"

**In 2045...**

With a satisfied smile, McKay cleaned his plate and took another sip of the old whiskey he had hidden away as long since forgotten memories returned slowly.

"Rodney, that was a good meal…"

"Glad you enjoyed it" He said with a smile.

"Anyway, I heard that when you got to the bridge… you where a little pissed off about being left out of the mission"

"To say the least, but Cole had a way of cutting past all the crap"

"Yes she did" Sheppard said quietly.

"Why you two never got together I don't know…"

"Actually…" He smiled.

"You're joking… right?"

**In 2015... **

**December 22**

Night time fell over the city of Atlantis as from the shoreline of San Francisco the ancient city illuminated before them as a brilliant clear sky, a full moon and calm waters made for a perfect photo opportunity for many of the residents of San Francisco. Word had travelled around the newest Tau'ri ship that Rodney McKay had been taken off the crew for the upcoming mission as he quickly made his way through the new ship towards the bridge. As he entered he stopped at the doors and looked around, clenching his fists slightly as he saw the new commander of the ship he walked towards her.

"Alright, what the hell are you playing at…"

Slowly Cole turned around in her seat as she saw McKay looking down upon her with anger in his face.

"Excuse me?" She said with a smile. "I was under the impression this is my mission to run… not yours"

"Yeah? Well we all make mistakes Cole… But to be replaced by Zelenka? No… I'm on this mission"

Nodding slightly she stood and placed her hand on his arm as she turned him to follow her towards the nearest exit, a small briefing room off the left of the main bridge.

"Rodney, I know you designed this ship… and you know her better then anyone"

"Yeah, that's why I should be on this mission" He barked.

"Listen, I met Karen… she's beautiful Rodney"

"I know…" He smiled.

"But you're also getting married in four weeks. I made her a promise that you wouldn't be on the mission"

"_WHAT?_" He yelled.

"I'm sorry Rodney; we're using a ship that has never been tested in combat… hell we don't even know if her engines are going to work yet. Once the engines are engaged we could just blow up on the Pier, I want you to be safe, besides John is going to need you here on Atlantis if the Alliance makes a run against Earth"

"Are you sure?" He said with a smile.

"Perfectly, we'll be fine without you" Laughing slightly she looked up at him. "You know in a strange way… you remind me of my Grandfather"

"Is that a compliment?"

"Yes a big one… he taught me everything I know, about everything. How long before this ship is ready to launch?"

"I can have her ready to launch in… twelve hours"

"Is that the best you can do McKay?"

Laughing slightly he looked down into her eyes; it was as if the spark in her eyes had returned slightly and the woman he respected was once again standing before him.

"Twelve hours is the best I can give you"

"Alright, well I guess I'd better leave you too it"

"Of course. You know Ronan was right about one thing, you and Teyla are so much alike"

"I'm honoured… I know Ronan and a few of the others always spoke highly of her, I also read most of your mission files in the past. I would have liked to have met her"

After leaving the new ship, Cole walked the corridors of Atlantis, although she had not been in the city for over a year, her memories of the city were still as fresh as the day she left. After a slow walk around the city she finally stood outside the door to her quarters, for a moment she leaned against the wall facing her door as she thought about the upcoming mission, finally she had made her choice.

Darkness filled the room as he lay almost asleep on the long sofa as papers and data tablets scattered around the room. As he almost drifted into the calm of sleep the door alarm chirped into life and brought his attention back to the reality of the past days.

"Ohh… what? What do you want?"

Pushing the many files aside he climbed off the Sofa and limped towards the door, as it slide open he leaned out of the door as a face appeared around the door frame smiling slightly.

"General, may I come in?"

"What, umm of course"

Pulling a bathrobe around him, he stepped aside as the former Colonel entered his quarters and looked around with a slight smile.

"Good to see nothing changes"

"What do you mean Cole… what are you talking about?"

"You know, I've never been in your quarters… but it's as messy as your office"

"Have you come for anything specific… or are you just here to annoy me?" Sheppard yawned.

"Perhaps a little of both" She laughed. "May I sit down?"

"If you can find a place, you wouldn't believe the reports I have to read. Coffee?"

"Yes, thank you"

A few moments later Sheppard returned from the back room with two hot cups of coffee, smiling slightly she took one of the cups from him and took a sip.

"Strong, black… thanks"

"You're welcome; I assume McKay has been complaining about being left out of the mission?"

"Yep, once I explained it too him he was fine. His fiancée is gorgeous… lucky I'm not into women" She laughed.

"She's been with us for two weeks before he even worked up the nerve to speak too her… finally about two months ago he proposed too her"

"Why did Beckett leave? I mean aside from another job"

"I don't know… he drops by from time to time. So why are you here Jen… what are you upto?"

"Well, as you like to say… it's a long story"

Slowly she stood and sat next to him with a smile on her face.

"What?" He laughed.

"Once this mission is over… I'm leaving the military, permanently…"

"You've said… a few times, Cole what the hell is wrong with you?"

"Come with me John… Just, just leave this city and come with me"

Laughing slightly he stood and walked around the room until he looked back at her and replied.

"Who put you up to this, Ronan, Zelenka? No McKay… I bet it was McKay"

Laughing she walked towards him and stood almost pressed against him as she replied while she looked up into his eyes.

"No one John… I'm serious"

With a smile she stepped back removed her top as his jaw almost hit the floor she reached up and kissed him softly.

"Like I said… Come with me"

Dawn broke over the Ancient city, as the new starship was ready leave the planet for the first time. Stood in the control centre, General John Sheppard smiled almost from ear to ear as he looked at the starship on one of the screens before him while on a separate screen the bridge crew of the ship began to call off readiness for mission launch.

"Atlantis Flight, this is Vengeance… We're ready to launch"

"Confirmed Vengeance… Good luck and god-speed" Sheppard said into the microphone.

It appeared as if she had looked up directly at Sheppard as she smiled and nodded.

"Helm, disengage all moorings, walkways, umbilicals and external power sources"

"Aye sir, switching to internal power… now"

Quickly the helm officer closed his eyes as for the first time the vessel switched to internal power while all of the consoles rang into life. Smiling too herself Cole looked around and nodded at Ronan as he sat at the weapons console.

"Vengeance you are clear for mission launch, activate your thrusters and proceed towards the first waypoint"

"Confirmed McKay, Helm engage thrusters… sub-light engines on standby… FTL Drive at station keeping"

"Confirmed Cole… we're gaining altitude…"

"Atlantis, this is Vengeance… we're airborne and clear to navigate. Activating cloak… now"

Almost as if it was inside a snowstorm the vessel disappeared as each 'Snowflake' caused a section of the ship it touched disappear until finally the whole vessel could not be seen nor detected by any sensor equipment.

"Sheppard, this Cole… remember my promise"

Blushing slightly he nodded at the screen as McKay looked up at him with a questioning look and half smile at the same time.

"Confirmed Cole… just get that ship back in one piece"

"Understood… Vengeance out"

It almost appeared as if a Hyperspace window had opened at the very edge of the atmosphere and quickly closed while the Atlantis crew sat back in their seats and looked at Sheppard for some answer to what the former Colonel had said.

"What was that about Sheppard?" McKay asked with a smile.

"It's private… Don't you all have work to do?"


	4. Chapter 4

**In 2045...**

Coughing for almost ten minutes straight as blood began to trickle from his nose and mouth, the retired General had been moved to a private room in the medical quarters of the great ancient city at the President's request while the doctors stabilised his condition. Outside the private room, President McKay stood talking to a young female Doctor in what appeared to be an intense argument until finally they walked back into the room. While the president stood at the foot of his bed the young doctor walked too his left as she pulled a chair too his side.

"General Sheppard, my name is Doctor McKay I'm your physician"

"McKay?" Sheppard said with a smile.

"Yes, we've met before sir… that was a long time ago"

Laughing slightly he struggled to sit up as he recognised the young woman before him.

"Samantha? You're little Sammy McKay?"

"Yes sir, that's me" She laughed.

"Good to see you inherited your looks from your mother and not that ugly bastard, right Rodney?"

"Ohh shut up John"

Forcing a smile Rodney walked around to his daughter's side as she straightened her tunic and looked directly at him with sorrowful eyes as she spoke.

"John, it's progressed further. I'm sorry; there is nothing I can do"

"I know Lil'Mac"

"You do?" Rodney said startled.

"That's why I'm here Rodney…"

"Sir, you should consider calling any family members to be…"

"Sammy, this place _IS_ my family"

As a doctor she had gotten used to giving patients bad news, but this one case seemed to hit her hard, not only was John Sheppard a friend of the family, he was also the godfather to her and her twin sister.

"As a friend I-I shouldn't be on this case sir, but I will stay with you for as long as you want"

"Thank you, how long do I have?"

"A day, maybe two at the most. You'll start to notice the effects as time goes on… I'm sorry Uncle John"

"John, I've called Karen and Jenny… they'll be back as soon a possible"

"Thank you Rodney, do me a favour?"

"Anything, just name it" He said as he sat down on his old friend's bed.

"Get that bottle…"

"What bottle dad?"

Sighing slightly the president lowered his head as he spoke to his daughter, since 2020 any alcohol above 20% had become illegal on earth yet having stored away a bottle of old Scotch Whiskey without the appropriate licence to do so could have the President up on charges if it was made public, however at the moment he did not care about his seat of power in the light of the imminent death of his oldest friend and military mentor John Sheppard.

"Alright dad, do what he says. But do me one favour?"

"Of course" He smiled.

"Save me a glass"

**In 2015... **

**December 22**

The mood around Atlantis had changed since the departure of the new ship, it almost appeared as if the Tau'ri where once again back on track to reclaim the galaxy they had fought and died for over the many years since the first mission through the Stargate in mid 1990s . From alliances with Teal'c's Jaffa fleet to the rising power of the Langaran forces and the many friendly races they had encountered over the years, the Tau'ri where fast becoming a powerful force within the galaxy. Sitting alone in his office Major General Sheppard sat looking at the empty screen on his personal computer thinking about the night before with fond memories and a large smile on his face, thinking about the long night he spent alone in his quarters with former Colonel Cole. Yawning slightly he began to type on the empty word processor page before him.

_From the Office of_

_Major General Jonathon Sheppard._

_It is with a heavy heart and the deepest of regret that I write this letter to my superior officers._

_With regards to my status as leader of the First Tactical Defence Force and Commander of the city of Atlantis in which I have served for many years, I tender my resignation from the Tau'ri Defence Force to be placed in effect by the end of the current solar year._

_As you will now be aware, the final strike against the Clone of Jack O'Neill is now underway by the recently launched prototype Starship completed at this facility known as Vengeance. Operated by a specially selected crew, this vessel will bring the renegade Clone back too Earth to be placed on trail for treason against the Tau'ri and our allies._

_Until an appropriate replacement can selected, I will place this great city and it's staff under the joint command of Colonel Ronan Dex and Dr. Rodney McKay whom by the time you read this letter will be promoted to the rank of full Colonel. Once again, I apologise for any problems this may cause._

_Major General_

_Jonathon Sheppard_

_Commanding Officer, Atlantis._

Smiling to himself, he read over the letter before he saved the file to the computer, leaning back I his chair he ran his fingers through his hair as a voice called out from the door.

"You look happy for the first time a weeks"

"Just thinking Rodney, that's all. Any reports on the ship?"

"Not yet she's under radio silence as per orders, best guess it will take a day to reach the planet… assuming the Clone is still their"

Leaning forward he motioned for his old friend to sit in the nearest chair as he reached into his desk and pulled out a bottle of whiskey with two glasses, as he poured out two large measures he handed one to McKay as he sat in the chair.

"You know, it's times like this I hate being in command of this city"

"I know what you mean, that's my ship. I should be on it"

"Perhaps, but she's right Rodney. Besides Karen would kill me if anything happened to you"

"She's a real spitfire…"

Laughing slightly he took a sip of his drink before he continued.

"Have you ever seen her make toast?"

Holding up his left hand he breathed on an imaginary slice of bread on both sides as Sheppard laughed slightly.

"I'll tell her you said that"

"I wouldn't. So what happened to you last night? I thought you wanted to hit a few golf balls"

"Umm… something came up" He replied behind his glass.

"I see, I hope it was worth it. I still want to break your distance record"

"Ohh, it was. So what do you have planned for this evening?"

A broad smile slipped across McKay's face as he placed his glass on the desk before him and leaned back in his chair with his arms crossed behind his head as he replied.

"Well, Karen wants me to cook tonight, I got hold of a bottle of very expensive wine, some candles… silk sheets, figure it out"

Smiling McKay leaned back further and lost his balance, as he fell backwards Sheppard laughed aloud as he looked over the top of the desk.

"Good job she's a Doctor"

Looking at the chair McKay joined in the laughter as he stood and bowed slightly before pulling the chair upright and sitting back down quickly.

"Never tell anyone that happened"

"Ohh I promise... scouts honour!" He mocked.

"You where never a scout"

"I know!" He laughed.

**In 2015... **

**December 23**

The new vessel had been at maximum speed for almost eighteen hours as the ship tore through hyperspace towards its destination. Since being placed in command of this mission the former Colonel had ordered battle drills to keep the crew alert as Drill Master, Colonel Dex pushed the crew to perfect timing and beyond making the small crew the most effective crew they could be.

"Five minutes… best time yet" He growled.

Exhausted from the rigorous training Dr. Zelenka looked up at the large soldier as he gasped for breath.

"Thank you Ronan… If you'll excuse me. I am going to collapse in the corner and cry for a little while"

Hitting him on his back in a show of support Ronan looked around the gym at the exhausted marines before him and nodded as he replied.

"Nine hours intense training, I think you deserve a little break"

"Thank you"

Zelenka slumped against the corner of room and slid down as he gasped for breath slightly.

"Major Andrews, where is Cole?" Ronan said with a grunt.

"She left… about an hour ago. She… said something… about the launch bays" He said gasping for air.

Grabbing a towel Ronan wrapped it around his shoulders and left the small makeshift gymnasium and walked to the port launch bay. On the far side of the small bay, a single figure stood looking at one of the new Tau'ri designed Hyperspace Puddle Jumpers, smiling too himself he walked towards the ship as he spoke with a sign of respect for the former officer before him.

"Amazing aren't they?"

Almost jumping out of her clothes, she turned quickly as her long blonde hair whipped around and slapped her in her face.

"Dex, What the hell are you doing here?"

"You walked out on training"

"One of the advantages of being in command. Have you flown one yet?"

"Not yet"

Slowly she ran her fingers along the deep black hull of the smooth support vessel before her as examined the gentle curve of the ship.

"I never thought they would look like this. Sleek, smooth, perfect lines. It's hard to imagine these ships are designed to kill"

"McKay called them, '_An iron fist in a velvet glove_'"

"An appropriate idiom, I'm looking forward to shoving one down that asshole's throat"

The new design was a dark black, sleek vessel that reflected barely any light from its surroundings; like its mothership, it held no external lighting or view ports. An almost seamless vessel that appeared to be cast from one large piece, on the portside of the vessel a single entry could almost be seen. Yet unlike its Lantean designed processor, the weapons and engines followed the overall lines of the ship and buried inside the vessel. Six small indentations on the forward and aft part of the vessel indicated the weapons ports, four on the forward and three aft of the vessel.

"What weapons do this carry? I remember the original schematics showed the F-302 style weapons"

"The primary weapon on these are the 302 pulse weapons based on the Asguard tech, the secondary weapons are something new. Can you see the two larger ports on the forward half of the ship? They are a new type of torpedo style weapon. It can fire eight of these new weapons, two pulse weapons on the front along with two torpedo launchers on the front and two pulse with one torpedo launcher at the rear"

"Nice!" She smiled.

Ronan opened the hatch to the ship as it elegantly slide up into the hull it's self, stepping inside the entire vessel came to life as she looked around in awe at the design of the ship.

"Bridge to Commander Cole" A voice echoed around the launch bay.

"Cole here" She replied.

"Commander, we have picked up an encoded message"

"What is it Major?" She sighed.

"The vessel commanded by the Clone has been spotted near the Armagosa Anchorage. The USS Arizona has been attacked and requesting assistance"

"_DAMN IT!_" She yelled. "How long will before we can intercept?"

"From our current position? Four days maximum speed"

"_SHIT!_ Maintain radio silence"

"Yes Ma'am"

Slowly she sat in the pilot seat of the new jumper as she looked at Ronan's blank face and replied slowly.

"Watkins, maintain course and speed, maybe we can bring them too us. Dex, assemble your landing teams"

"Already taken care of… what are you planning?"

"A little homecoming for an old friend"

**In 2045...**

Doctor Samantha McKay, Chief Medical Officer and daughter of the President had sat by the side of the ailing former General since his arrival under her care in the infirmary earlier in the evening. Word had travelled about this ill condition as old friends had arrived to pay their last respects to the once great man and honoured leader of the Tau'ri. At his own request, he was moved from the infirmary to his old quarters for his final hours as Ronan and Rodney sat beside him as Samantha tried everything possible to keep him comfortable while the three old friends shared a bottle of scotch whiskey together. Laughing and joking about old times almost as if nothing was wrong, Sheppard finally looked at the young doctor as he clenched his eyes shut.

"The pain is back?" She asked with concern.

"No, the light. It's too damned bright"

With concern, she looked at her father and to Ronan as they all knew what was happening to the once proud warrior.

"Computer, lower the lighting by 50%"

Slowly the lights began to dull as finally Sheppard opened his eyes and blinked away the pain that he was feeling inside of his head.

"Is that better sir?" She asked with concern.

"Much, thanks… So Ronan, what where you saying?"

"Never mind…" He replied with concern.

The door to Sheppard's old quarters opened as Karen McKay and her daughter Jennifer entered quickly. As they walked towards him Jennifer, the youngest of the twins gently hugged him as her tears began to flow. Smiling slightly Sheppard looked at both the women and nodded with respect.

"Well, how was the… festival?"

"Great John, Just great. Rodney, are you drunk?" Karen said slowly.

"Just… Just a little" He laughed. "But I-I guess you don't want any of this"

Laughing slightly he waved the empty bottle of scotch in front of her as he picked up a second half full bottle, smiling slightly both the women stepped forward and grabbed an empty glass as Rodney laughed slightly as he poured out a glass for each of them in turn.

"Dad, I thought you didn't drink because it was against the law"

"Jen-Jennifer, I thought you better then that"

"Yeah, some rules are made to broken" Sheppard said with a slight cocky grin. "Hey Karen, did I ever tell you about the time that your beloved here fell off a chair?"

Quickly Rodney fired a harsh look at Sheppard and finally laughed as looked around the room, raising his glass he spoke aloud with a sense of honour he had long since lost.

"To old friends, present and gone"

"No Rodney…" Sheppard laughed. "Here's to Sam Carter, Doctor Jackson, Lorne, O'Neill, Landry…"

Standing slowly Ronan raised his glass as the rest stood and raised their glasses in toast.

"Woolsey, Teyla…"

"Beckett…" Karen replied.

"The crews of the USS Hammond, Apollo, Odyssey, Arizona, Daedalus…" Samantha continued.

"Bra'tac, Teal'c… C-Cole… and all those who had given their lives for the freedom we now enjoy" Sheppard said.

Choking back his tears Sheppard took a long drink from his glass and the others took a sip in turn.

"I think we should give the General some time to rest"

"No, I'm fine Sam…" He replied with a smile. "Jennifer, how is the guy of yours?"

"Alan? He's fine. He's taken up a position as Commander of Armagosa Anchorage, and he gave me this…"

Smiling she pulled a small ring from her pocket and passed it around. Quickly Rodney grabbed the ring examined it, the rare and precious metals glinted in the dull light as a small self illuminating gem light up with a slight green glow.

"I take it by the fact that you're not wearing this…"

"I asked for some time to think"

"Your mom did the same thing" He laughed.

"Liar, I asked you" She smirked.

"Give me a break… Karen he asked you… in front of the Stargate and everyone else, I've never seen a man turn as red as he did" Ronan replied.

"Wrong…" She laughed. "It was my idea,"

Seeing the look in McKay's eyes, everyone in the room burst into laughter as Karen walked towards her husband, for a moment it appeared like old times until they where brought back to the present by the coughing of the patient on the bed. Quickly leaping into action, Samantha and her mother jumped too his side as they pulled a pillow up too his back and sat him up right.

"I'm fine… god, I don't need a nurse maid"

"Shut up John, for once in your life do as your told" Rodney yelled.

"Is that an order Mister President?"

"Does it have to be?"

"Mom, Dad… Ronan, I think we should let John have a little rest. We'll be in the next room if you need us"

"Of course Sam, your right" Karen replied with concern.

Slowly they began to leave the room as John placed his head in his hands and laughed slightly.

"Ronan, stay"

"Of course"

"You haven't said much, even for you" He laughed.

"Sorry John, just amazingly… pissed off. I've seen you defeat just about every enemy. But to see you loosing this battle…"

"Hey, I'm gonna be around for a long time yet. You know Rodney left that bottle"

Smiling, Ronan sat next to his old friend and put his feet up on the corner of the bed and poured out two more glasses of the old illegal drink.


	5. Chapter 5

**In 2015... **

**December 23**

Silently the new Tau'ri starship exited hyperspace away from the planet as it continued along its course on full sub-light speed, the crew of the ship where under no illusions about the mission, especially as it could be a one-way trip, but if successful it could mean the end of the war once and for all. The renegade clone of Jack O'Neill was the main target for this mission however, his research into Ascension had to be explored.

Sat with confidence in the command seat, Cole looked over the reports from her chair side consoles as weapons, shields, status displayed on her left console as on her right side, scans of the system had begun to be displayed.

"Approach the system with caution helm, scan for any defences on the surface and in orbit. Select the perfect place for a landing party… Ronan, gather your men, I'll be joining you. Zelenka… take command"

"Commander?" Zelenka replied.

Although she held no official rank with the military, it was an unspoken rule on the ship that the honorary title of Commander would be given too her for the duration of this mission.

"I need someone up here who knows this ship inside and out. And someone I can trust with this beauty…"

From the corner of her eye she saw Ronan smiling slightly, laughing too herself she turned and looked directly at his battered and bruised face as she replied.

"What? Got a problem Dex? Want a rematch?"

"What? I said nothing!" He laughed.

"Alrighty then… "

"Commander, I've completed a full scan of the planet. Sensors are detecting one structure, I think you should take a look at this" Zelenka said with shock in his voice.

Both Ronan and Cole walked towards the main sensor readout, shock followed them in short order as the scans of the planet began to show just one structure in the centre of a large desert on the equator of the planet.

"Holy crap. Is it me, or does that look like"

"Readings confirm it Commander, it's an ancient warship, I have only seen a ship of this design in the ancient database back home. It was designed at the latter end of the Wraith war as a last ditch effort to defeat them" Zelenka said slowly.

"Is it space worthy?" Ronan replied.

"Sensors can not penetrate the hull. If it's sensors are working, they will detect anyone beaming down"

"Jumpers?" Cole said with a smile.

"Perhaps… assuming that ship is run by one or more ZPM, they could detect your approach"

Cole looked at the sensor display once more as a cold, dark look crept across her face.

"I have an idea!"

"Knowing you, it's either stupid and dangerous"

"It's both Ronan… Zelenka, I have a little job for you"

"What is it?" He sighed.

The plan set in motion all that was left to do was to make sure that Ancient vessel on the planet had plenty of targets to confuse its sensors, from the opposite side of the planet the Vengeance would launch eight modified sensor drones equipped with a cloak and programmed to remain in a specific formation. It was hoped that the energy signature the drones would be transmitting would confused the crew of the ancient vessel into believing that a large Tau'ri fleet had launched an attack on the planet allowing the landing parties to slip into the ship undetected.

For the first time in his career, Radek Zelenka sat in the large comfortable centre seat of the new ship, the smooth black leather of the seat groaned slightly as his weight shifted in the seat as he ran his hands slowly over the armrests of the elegantly designed chair. What ever had caused the unusual odour on the ship had remained within the ship as the sweet smell drifted in the slight breeze from the environmental systems. Taking a deep breath he gave his first order as commander of this unique starship.

"Launch the drones…"

"Aye sir, drones away"

From the main veiwscreen at the front of the bridge, a slight flickering could be seen as eight of the drones passed through the cloak.

"Sciences, give me real-time and sensor readings overlaid"

"Bringing it up now Doctor"

A one quarter blue coloured mesh ball covered the desert world below with a flashing green square in the centre of the ball that signified the Ancient vessel below, while eight red dots formed up in a large fleet like formation. from the Science station an alert signal caught the operator's attention as she leaned into examine the readings.

"Doctor, the drones are being scanned from the surface"

"Excellent, thank you Talia. Bridge to bays one and two, the drones have been detected…"

"Perfect, opening bay doors. Cole to Jumper Two, activate your cloak and stand by to launch on Zelenka's Command"

On the main viewscreen, two small squares appeared with internal displays of the twin Tau'ri Jumpers, laughing slightly the sciences officer controlled the drones along a pre-determined flight path as the order was given to launch the twin support vessels. Screaming from both launch bays, the two jumpers joined formation and followed a designated flight path around the '_Ghost Fleet_' on a shallow path to enter the atmosphere of the planet below.

In the pilot seat of the first Jumper, Cole smiled too herself as she piloted the vessel with ease, as they approached the ground, she could hear several of her landing party asking for her to pull up as the ground rushed towards them at high speed.

"Pull up. Cole _PULL UP!_" Ronan screamed. "_COLE…_"

A Slight bump rocked the jumper as they levelled off mere inches from the ground. Laughing too herself she looked back at the frightened away team as she called out.

"Anyone wanna do that again?"

"Cole, you're damned crazy. What the hell do you call that, suicide?" Ronan moaned.

"Funny, but no. Coming in under their sensors, I hope"

On the horizon the large Lantean vessel came into view as both jumpers held position while they established a count of all weapons and personnel.

"Damn that thing is huge" Cole said in awe.

"Dragon one, this is Dragon two. Respond…"

"Go ahead D-2" Ronan replied into the radio.

"We're picking up a power surge from the ship… it looks familiar"

"Stand by D-2"

Slowly Ronan and Cole stood in shock as the rest of the mission team stood and looked at the ship on the horizon. Streams of yellow and orange coloured objects streamed out of the Ancient craft before them, circled the starship and finally disappeared into the sky above.

"Is it my imagination, or does that look like they are…"

"If you're thinking they look like Drones…"

"Sensor readout confirms it sirs, they are Drones" Called out a woman behind them.

**In 2045...**

The night had been a long and difficult one for the medical staff and close friends of the old general, throughout the night his heart had stopped three times and his breathing had become short and shallow. Yet each time he seemed to drift away, he could be seen smiling at something that wasn't there. An almost calm and serene smile that echoed with love and affection, to the medical professionals in the room it was something they had seen in the past, in the eyes of those who where about to die.

As the sun arose over the surface of the ocean that surrounded the city, preparations where underway for the memorial service to note the thirty years since the end of the Great Tau'ri War. All speeches had been written and approved by the military force that protected Earth and it's every growing sphere of influence. With his old friend, mentor and former commanding officer almost prepared to breathe his last breath, the President had become torn between his duty to the Tau'ri and his loyalty to his friends. With the Vise President back in the city, his next choice would be a difficult one as he called his running-mate into his office.

"Mister President, thank you for seeing me"

"Not a problem, sit please" Rodney said with a smile.

"What can I do for you sir?"

"Andy, I'm about to make a choice that will either make or break my Presidency"

"With all respect sir, what are you talking about?"

"A short time ago an old friend of mine returned to the city, perhaps for the last time"

Nodding softly the Vise President replied with a sorrowful voice.

"I know sir, I have heard about former General Sheppard, my condolences sir. Is can I help in anyway?"

"That's why you are here Andy, I want you to give the memorial speech in my place"

"Me sir? They will be expecting you and your family to stand in front of the gate, not me"

"I know that, however we don't expect Sheppard to survive the end of the day. I owe it too him to be at his side when…"

"I got it sir, I would be honoured. May I give your apologise to those who are expecting you?"

"Of course. Thank you Andy, one more thing. I want you to do me one more favour"

"Anything… just name it" He said slowly.

"I owe John more then I can ever say, many of the old missions are classified even today. I want a full state funeral for him. Full honours Tau'ri flag at half mast. Contact General Mitchell, tell him to dig out six of the old F-302 fighters for a flyby along with six of the new Viper class fighters"

"On it sir… I'll contact the General right away sir"

Nodding with respect for his friend and Commander in Chief, the Vise President left the office. Since the end of the war, former SG-1 leader and head of the Starship Construction yards, Cameron Mitchell had taken up the position left by General Sheppard upon him leaving the service. Although command of Atlantis fell upon McKay and Ronan, Mitchell commanded the majority of the Tau'ri forces from the old Stargate Command facility, something which drew a barrier between the old friends and comrades many years ago.

**In 2015... **

**December 23**

In the aftermath of the attack on Earth, the clone known as Jack had lost more then he could have imagined. After the news of the death of his wife at the hands an unknown assailant, he quickly turned against his allies in the Lucian Alliance as once again it began to fracture and split into two halves. Controlling a large fleet of Lucian Alliance and former Free Jaffa ships and their crews he began a war against the remaining Lucian Alliance that would leave very few survivors. However, unknown to Jack, his wife Gemma and newborn son Charles Tyler was safe, hidden away from the ever growing gaze of Jack's empire.

Footsteps echoed through the halls of the small ship, although he commanded some of the largest and most powerful vessels in the known galaxy, he still preferred to use this old Al'kesh ship for short distance trips. Although he still looked forward to returning to his pride and joy. A Starship designed by the Ancients themselves, buried under the sands of a forgotten world for a millennia, a Dreadnought class vessel, one of only a few built and the only one known to have survived. Discovered many years ago by his predecessor and mistaken for an old crashed vessel, now brought back to life by the vital Zero Point Module power source, and the perfect place to continue his research into ascension and the ultimate power that it brings with it.

"My Lord, we are approaching the home planet however, I am detecting weapons fire from the surface to orbit"

"Show me!"

Almost unrecognisable, Jack stepped closer to the screen fitted to the flight deck of the ship. Being known as public enemy number one, had it's drawbacks. His picture and details had been posted on every planet within the reach of the Tau'ri, so a change in appearance was needed once in awhile. Wearing dirty and stained old clothes with a dirty stubble look to his face he was barely unrecognisable, more so with the foul odour of many days without cleaning, all a part of his disguise so that no one would spend time near him.

His face turned to shock as he saw what appeared to be Eight Tau'ri Cruisers on the sensor readout, yet as they approached, nothing could be seen but small explosions caused by the Drone weapons launched from the surface.

"According to the sensors My Lord, the enemy fleet is all around us"

"But nothing here… get me down there… NOW!"

Once within range of the ship, jack stepped onto the ring platform as it locked onto the Ancient vessel on the surface. Although few Ancient warships had ring platforms, Jack had personally ordered that at least one be placed on the warship, now his decision had paid off as he materialised behind the bridge of the vessel. Almost the instant the rings cleared he broke into a full run towards the bridge, as he entered he yelled with all the authority of his status.

"_STOP FIRING YOU IDIOTS!_ You're shooting at a Ghost Fleet"

"I do not understand My Lord" A Jaffa replied nervously.

"That's not unusual, is it? Scan the immediate area for anything unusual. Sensor echoes, atmospheric distortions… anything"

"Scanning my lord. Nothing unusual, however I am detecting an open hatch on level G section 14-a"

Smiling too himself he looked around the bridge as the crew of Jaffa, Humans and other species awaited his next order.

"I hadn't expected such a brash move from General Sheppard…" Smiling he looked around at the crew before him "… Of course, the lovely Colonel Cole once again"

"My Lord, should I order defensive teams too…"

"No, stand down all defensive teams, switch internal sensors to a passive sweep. Have teams three and seven report to Lab One… I will be along shortly. They have a ship in orbit someplace, find it… nothing more. Just find it"

"Yes, My Lord" The Jaffa bowed.

Carefully, the boarding teams entered the ship one at a time, as each of the entered they took up defensive positions around the hatch they had entered through until all team members where ready, using hand signals, a large male Marine signalled for the hatch to be closed and the two Tau'ri Jumpers to leave the area and wait until called for.

Once more with hand signals, Ronan Dex, the ranking officer on the mission gave his orders, for the teams to split into two groups. Although they all knew the mission profile, team two was ordered to locate the research on ascension while team one along with former Colonel Cole would locate the renegade clone of Jack O'Neill.

Splitting into two groups the teams disappeared into the darkness of the ship as the two new Jumpers moved away from the dangerous ancient vessel. Her blood began to pump around her body as she followed the large Pegasus Galaxy alien through the ship, the layout of many Ancient ships remained the same so it was hoped that they could find their way around this vessel with ease.

"Do you have any idea where you are going Dex?" She moaned.

"I know it's been awhile Cole, but please… shut up!"

"Sorry. Déjà vu right?"

"What?" He mumbled.

"I think it was about three years ago now when you, me, Beckett and McKay broke into that facility where Sheppard and President Hayes where being held"

"That was fun. Who would have guessed a pilot is afraid of heights"

"Hey, it's not uncommon" She Growled. "How far do you think too…"

"The Bridge? No idea, you know the odds of the Clone being here are very high" He whispered.

Silently they walked through the next corridor, with each turn the architecture on the ship reminded them more and more of the great city they came from, as they turned the next corner a brilliant flash of bluish-white light hit them as their senses began to overload while the darkness quickly overcame them as the final moments of conciseness Ronan saw a blurred image of what appeared to be the clone dragging the unconscious body of Cole away from the group as his vision clouded over and darkness claimed him.


	6. Chapter 6 (Caution Advised)

**In 2015... **

**December 24**

Darkness and light, a mixture of two opposites danced around each other before her as she began to regain her senses, but now another sense, cold. Almost an extreme cold, as if an icy wind blew through her clothes, her flesh and bones while the bright spots of white light danced before her eyes for a moment. No, now something different, a sound a loud sound that almost deafened her ears as it continued while the light and cold fought her at every turn, yet now something different as her body attempted to move away from the unknown touch that ran down her body yet to no avail as an unknown force held her in place. Slowly her hearing began to return as her own breath could be heard while the brilliant white light began to expand, form shapes and colours; slowly the feeling began to return in her arms and legs as they began to struggle against what ever had held them in place. It seemed to last for hours as an intense pain continued to run through her body while all along it appeared as if her senses where being controlled from some other place, yet now something different. A sound, no a voice… words began to form, no, it was not a sentence it was something different… a scream, her scream.

An explosion of sound brought her back to consciousness as the cold air blew past her, and now something different, the horrid taste of blood filled her mouth and throat as the sound of laughter echoed around the room. Now finally a single voice, a soothing and familiar voice called out to her. It had almost appeared as if the voice had rang out through the room, yet no sound of an echo could be heard, this was something different, something attempting to make direct contact maybe? Her mind ran wild as the voice spoke in a familiar and soothing tone that made her whole body relax. '_Jenny, let this happen… Trust me_' Her mind snapped free as her vision cleared in an instant, pain ran through her body as she looked around. Both of her arms where held in place out to either side by an unknown force as her legs where separated by a similar force. An icy cold breeze appeared to blow though her as she hung almost two meters off the floor by some indivisible force, yet the one thing that shocked her the most, as she looked around her clothes had been removed as she appeared to hang in front of the Renegade Clone himself.

Laughing slightly the young man walked towards her and ran his right hand over her left leg smiling with pleasure at the discomfort she was feeling, almost instantly she attempted to move away only to be forced to remain in place by what ever was holding her.

"You know, this was a lot easier with you out for the count. But not as much fun, but I still like what I see" He smiled.

"Where am I?" She growled.

"Safe, for the moment… you have no idea of what you are, do you… Jennifer Anne Cole?"

"So you know my name, let me down from here… I'll show you more"

Smiling the Clone walked around her and smiled as he looked at her naked body, taking in a mental picture of her every curve.

"Ohh, I can see more then you think…"

"Jennifer Anne Cole. Civilian, of the Tau'ri… Formerly…"

"Ohh stop the P.O.W routine Cole, I know what you are"

"Then you should know to let me go, if you know who I am. Then you know the instant I'm released from this cage… I will cut your damned heart out for what you did to me!"

"Ohh my dear, we've only just begun" He said darkly. "You really have no idea what you are capable of, what you really are do you? You have only just begun to access the true abilities within you, you can almost hear the thoughts of others I assume? Doctor, prepare her for the examinations…" He said to the old woman behind him. "I'm afraid you will not survive the final procedure Miss Cole, but know this… once I am done with you, I will launch this ship… your little Ancient city will be no match for this vessel. As for your General Sheppard, I have plans for him also"

As he laughed slightly, she struggled against her invisible bindings while snake like tubes began to immerge from the walls and ceiling of the room she was being held in by some invisible force. On the ends of each snake like tube, a long sharp needle appeared as they punctured into her body while a blood-curdling scream exploded from her lips. Smiling too himself, the clone walked back towards the console before her and looked at the readouts.

"What do you see Doctor, are we correct?"

"Readings are coming through now My Lord… A.T.A count… off the charts, stability 100%, compatibility 100%… possibility of success… 100%"

"Excellent!" Jack laughed.

Slowly he looked up at the young woman hanging from the room as pain ran through her body he smiled slightly.

"Doctor, we can not have her pass out at such a critical moment. Deactivate her pain receptors"

"My Lord… that could kill her"

"Do it, now… or will find someone who can. I am sure Doctor Monroe would love to stand here looking at this beautiful naked young woman"

"No need to call her my lord, deactivating the subjects pain receptors… now"

A large sigh crept across her face as the intense pain she was feeling from the needle-like tubes burrowing into her body had stopped in an instant. Although the uncomfortable feeling of the tubes moving around inside her body remained, she could still feel something, almost as if she was about to give birth to something horrific.

"Doctor, estimate on how long it will be before we can begin the procedure?"

"I would say two hours my lord. I wish to run a few more tests on the subject before we begin"

"As you wish, keep me informed on your progress. I will have Monroe prepare phase two of this objective. Ohh, our lovely guest… forgive me Colonel Cole, but matters require my attention elsewhere. It is a pity that you will not survive, you are very beautiful and would make an excellent partner, who knows… perhaps I will make a clone of you, for my own needs with a few alterations of course, I think I will make these larger" He laughed as he pointed to her chest.

"That's what all this is about, Cloning?" She yelled.

"No, and yes. Ironic that you are not only the one I seek, but you also are the answer to the Asguard cloning problem, pity my creators never found you, pity they are all dead. That is why I chose you, that is why you are here now"

She almost laughed as she listened to the insane ramblings of the man before her, from what she had read in the files of General O'Neill this man was a direct clone of him, only his grow was stunted by the Asguard, however he was nothing like the man she had read about so many times. This man was almost delusional to the point of being insane, yet as the doctor at the work station before her activated the controls she could almost feel his thoughts of loss for his wife and child, while a fifth needle and tube began to burry it's way into her back and work up her spine, had her pain receptors not been deactivated some how, she would have passed out from the pain it delivered.

"I would rather die a thousand times over, then you have any part of me"

Quickly he cleared the distance between the two of them as he jumped onto the platform she was being levitated from and grabbed her by jaw.

"My dear, I will have you… or at least, some part of you"

It happened almost as if in a horror movie, although she could feel nothing, she could see what he was doing to her as he climbed up too her and ran his tongue from her shoulders, up her neck and bit her ear slightly.

"You will have to kill me first"

"No my dear…" He whispered in her ear. "I'm going to kill you… during. Over and over again…"

Slowly as if caressing every curve of her figure, he ran his hands down her sides to her thighs and smiled as he pulled her close to him and whispered in her ear once more.

"… Until one of your clones gives herself to me"

If her senses where her own she would have shivered at the thought as he jumped down to the floor and looked at the old female doctor working the controls.

"Let me know when she is ready Doctor, I have a ship to find" He smiled darkly.

"Yes my lord"

As he walked to exit the room, Jennifer's mind raced once more, it was almost as if her lips had taken over and she was purely observing her own body as she spoke.

"You can't kill me Jack"

"And why not?" He bowed as if to mock her.

"If you do, you will never see… your wife and son again"

Once again, he cleared the distance between them as he ran towards her and grabbed her jaw and squeezed with all the force he could.

"My wife and son are _DEAD_ because of you and your… kind"

"No…" She laughed. "… They are alive, hidden in a safe place, away from you and your enemies"

"You _LIE!_" He growled.

"Can you take that chance?" She laughed. "Can you take the chance that I am lying? Your son, Charles Tyler… Born August 3rd 2013... Infirmary on Atlantis, weighed seven pounds five ounces. Eyes blue, hair black a small genetic birthmark on his left arm. Mother Gemma Claire Winterman, daughter of the General that _YOU_ killed on Atlantis… she has been made aware of your duplicity and that you murdered her father. How do you think we knew that you where here Jacky-Boy? She gave us this place in exchange for sanctuary"

"She would never give me up for Earth"

"She knows you killed her father, and she thinks you are going to kill her and take her son" Jennifer laughed.

"You're a lying bitch…" He yelled.

"Maybe, maybe not. Do you want to take that chance?"

Laughing slightly, Jack walked towards the doctor at the console and took a deep breath before he spoke.

"Cut her loose"

"My lord?" She said quickly.

"You have what you need for now, analyse the readings and report back to me… I have a feeling that this young woman will be around a little longer then expected"

"Yes My Lord"

Jack left the examination room, his body language showed stress and anger as the doors close behind him. The last thing she expected to happen, happened before her eyes. The elderly woman quickly locked the door from the console before her as she worked a second console. Almost instantly the many tubes attached too her began to retract as they slide out of her body. The uncomfortable feeling rang through her as she began to feel physically sick at the feeling until finally the warm glow of blood pouring out of the slices throughout her body. Almost the instant the tubes exited her she fell to the ground hard as the old woman spoke nervously.

"Easy Colonel… take it easy. I don't have much time"

With every piece of strength she could muster, Cole jumped to her feet and grabbed the old woman by her throat.

"You damned right you don't" She yelled.

"Colonel… take it easy… I'm Tareth Aileen. Langaran… Security"

Shocked, Cole released the old woman as she fell to the floor coughing.

"You're stronger then I thought… I was placed here over a year ago"

"Talk, now… what the hell is going on?" She barked.

Slowly the old woman scrambled too her feet as she passed the Cole what appeared to be a medical gown.

"I was sent here a little over two years ago. First Minister Quinn believed that the young Jack was planning to attack Langara"

"He did, I was their" Cole said quickly.

"I know, I saw… nice work. He was looking for something… a piece of equipment stored away for a millennia… forgotten by everyone. The final pieces came when he attacked Atlantis last year, he's working on Ascension and Cloning technology. Imagine a clone army with the abilities of semi ascended beings…"

"What the hell are you talking about?" She growled.

"Anubis, the Goa'uld was part ascended, right?… right! Many years ago Doctor McKay was accelerated by a so called… Ascension machine, during which time he displayed telekinetic, telepathic and advanced healing techniques as well as enhanced intelligence. Jack took several important parts of _THAT_ Machine from your city and incorporated it into his own"

"He's built an ascension machine?"

"No, one was already on this ship. But it was incomplete" She said quickly. "He rebuilt it"

"Where do I fit in?"

"Watch!"

Quickly the old woman walked back towards her console and activated the device once again, from the ground upto the ceiling a swirling image of colour and light appeared in holographic form.

"This is a normal readout of a normal human being…"

Slowly the image darkened and became green as a second image was overlaid on top in bright red.

"This is Jack's readout, do you see the high peaks that indicate a high ATA count?"

"Of course…" Cole replied.

"Watch this, this is yours"

Once again a third image appeared in bright yellow and overlaid on top of both the holographic images.

"The peaks are higher, but appear shaky and broken like Jack's, is that normal?"

"No the broken peaks on Jack's readout confirm the fact that he is a Clone… of Asguard design"

"I am not a god damned clone" She barked.

"I know. However, I don't understand why your peaks are broken like those of Jack's readout. But your ATA count is off the charts… these readings confirm that you are closer to ascension then anyone I have ever seen"

Laughing Cole walked around the console and looked at the holographic readout before she turned back towards the old woman before her.

"I don't believe you, but if you are who you say you are… where is my team?"

"The Pegasus Alien and the others are being held on the other side of the ship. Jack will begin experimenting on them once he has what he needs from you"

"Which is?"

"Blood… DNA anything he can use to make his clones, however I have heard rumours that he has begun to use the machine on himself… at a lower setting"

"I have to stop him… help me" She said slowly.

"I can not do that, I have to…"

"Help me, please. What do you think will happen once he has what he wants from me? He'll kill you, I've known people like him Aileen… he will burn your world once he has what he wants"

"You don't understand Colonel… but you will soon, remember one thing. I never wanted to hurt you… I'm just doing my job"

Quickly the old woman grabbed an old style syringe and injected the former Colonel in her neck, confused and angered, she collapsed to the floor as her vision began to fade once more.


	7. Chapter 7 (Caution Advised)

Hidden under the new highly effective cloak, the new ship called Vengeance orbited the planet with the Ancient vessel within sensor range. The entire sensor drones had been destroyed by the Ancient weapons launched from the large dreadnaught as an active search of the orbit of the planet was being performed by support craft launched from the Dreadnought itself. Although the two mission teams where ordered to maintain radio silence while on the surface, the command crew of the new ship became more eager for some form of contact as each second had past.

"How long now?"

"I wish you'd stop asking me that Doctor, but its five minutes since you last asked. That makes it one hour fifteen minutes. No contact as of yet"

Nervously the communications officer sat at her console monitoring all channels too and from the planet below, suddenly the young engineer turned communications officer froze as a voice began to break past the many different channels.

"Sir, detecting a message from the surface… I can't quite clean it up"

"Let me hear it" Zelenka said eagerly.

Through the many different channels, one voice began to grow more and more dominant, a voice made the temporary commander shiver slightly.

"I know you are listening to me, it will not work. Your away team has been captured and executed; your subterfuge with that ghost fleet was detected. As you have seen from my display I have the full power of this vessel at my disposal, we are zeroing in on you position as I speak. For the good of your ship and ship and crew… give it up, once I find you… I will destroy you"

The voice was unmistakable; it was the calm yet dark and twisted voice of the O'Neill clone.

"I take it you do not want to reply?"

"Not a chance…" Zelenka replied swiftly "If we reply, he can lock onto our position. Ignore it"

Running his fingers through his hair, Zelenka sat back deeper into the chair as he clenched his fingers quickly in an attempt to hide his trembling hands.

"Oh my god… sir detecting four motherships exiting hyperspace… they are firing at the ship on the surface"

"_WHAT!_"

Quickly he jumped out of his seat and ran towards the sciences station as a voice broke through the speakers on the bridge.

"This is Teal'c of the New Jaffa Alliance, for the murder of Bra'tac you have been sentenced to death"

Hitting the wall before him, Zelenka looked around at the seasoned officers before him as they looked back at him for his orders. For the moment it was unclear if the away teams had been captured and killed, yet he knew that the four ships of Goa'uld design where outmatched by the power of the Ancient ship on the planet surface.

"Orders? Doctor Zelenka… orders?"

It was unclear if it was fear that had gripped him, or if it was, the fact that he was overwhelmed by what was unfolding before him as he froze to the spot. Quickly, the weapons officer jumped too her feet and began to yell out orders as she assumed command of the vessel.

"Drop the cloak, raise shields, arm all weapons… you, coms girl contact the lead ship now!"

"Yes ma'am" She replied. "Channel open"

"I am Major Amanda Dickens on board the Earth Ship Vengeance to Jaffa Fleet… _STOP FIRING_, We have people on the planet"

"Major, weapons fire from the surface!" Called out the science officer.

"SHIT! Launch all countermeasures; place us between that fleet and the planet"

"Tau'ri Vessel, this is none of your concern… move aside or you will be considered a legitimate target" Teal'c replied quickly.

Stepping into the centre of the bridge, she straightened her tunic as she stood tall.

"Teal'c, those weapons being launched are Lantean Drones… pull back"

"Not until we have our vengeance"

Two Jaffa vessels exploded from the surface weapons fire as the Tau'ri ship moved between them. Violently the ship rocked from side to side as drones impacted on the shields, Gliders began to launch from the remaining ships and screamed past the Earth vessel as it protected to remaining ships from the deadly weapons fire.

"Teal'c you can't win this one. Our primary shields are at 50% and falling, pull back… we'll cover you!"

"Not today Tau'ri…" He replied darkly.

Before she could reply, the communications channel ended as Dickens looked around the bridge; their position had been compromised by the actions of the Jaffa.

"Damn arrogant Jaffa…" She yelled.

"Major, the lead ship is taking hits… she can't hold out"

"Damn it!" She yelled once again. "Transport any survivors to the cargo hold and plot an escape course away from the planet"

"Major, what about the away team?"

"We'll be back for them, once away we'll reactivate the cloak and return to the planet"

Consoles began to explode as the primary shields began to fail, almost instantly the secondary shields activated however, the damage had been done to the ship as the sensors began to record section of the ship had been damaged severely as an area of the ship had had lost it's atmosphere as the hard, cold vacuum of space had invaded the ship.

"Major, we've been holed. Deck four, sections eight and nine. Emergency bulkheads are in place, forcefeild are holding"

"Casualties?" She yelled.

"Sensors are recording eight missing in that area"

"Damn it! Seal off the section, evacuate the out hull areas. Helm, get us the hell out of here _NOW!_"

Swiftly the damaged vessel disappeared out of orbit as the remaining Jaffa vessels followed. Sitting back in the chair, the acting commander fired a deadly glance at Zelenka as she spoke to the nearest officer.

"Get that man off this bridge; get him down to engineering now. Maybe he can actually do something about this damage. And someone turn off that damned alarm, Get me Teal'c NOW! I wanna know what the hell he was thinking"

"Yes ma'am… this way… _Doctor_"

Although her pain receptors had been deactivated somehow, she could still feel certain things. Perhaps it was her body readjusting to what ever they had done too, yet now as she began to regain conciseness once again something different a sound, something cutting close too her ear, a heavy breathing near her and something pulling on her hair as distant voices spoke with laughter. Now a terrifying feeling of hands running over her chest and stomach. No, she thought this was an invasion of her body, she was being attacked. The feelings began to return to her arms as a sense of cold metallic shackles around her wrists and ankles, almost as if she was being suspended once again off the floor. Anger began to swell within her as she attempted to drag herself back to consciousness, and now something different, something in her mind. A voice once again, familiar and soothing while in her mind's eye a face began to appear to her. All feelings of fear began to subside as she found herself sat in what appeared to be the front seat of an old bi-plane. The scent of the leather seat, the purring of the engine in front of her and the cool summer breeze blew her long blonde hair as she began to focus.

"What? Where am I?"

"Remember what I said Jenny, gently pull back on the control column and get some air under the wings. Feel the power of the engine, feel the freedom of flight… that's it, you've got it"

"What? Grandpa?"

Quickly she whipped her head around and looked on in shock at the man sat in the rear cockpit, it was her grandfather, he looked exactly as she remembered him when she was a child, when he taught her how to fly as a child. Yet something was different, she wasn't the child he was teaching, she was in her early thirties.

"What is this, Where am I? This is not real"

"Yes it is Jenny… you're doing it, you're flying"

"Who are you?" She demanded.

Almost the instant she spoke, her vision changed. Now she was stood in the Gateroom of Atlantis, yet it was dark. All the lighting had been deactivated with the exception of the active Stargate. Shocked she spun her head around looking for any sign of activity; she had read the reports of how the great city looked when it was first discovered many years ago, it appeared exactly as in the reports. With covers over the consoles.

"What is going on here, who the hell are you?"

From the Stargate a figure began to materialise and step into the city as more humans began to enter the city until finally the lighting began to activate. Shock ran through her as the men and women appeared to have walked through her, her jaw dropped as listened to the orders being given.

"Ohh my god, I know who that is… Doctor Weir?"

Quickly she ran towards the woman who lead the expedition and stopped in front of her almost in an attempt to speak to her, yet as before, she walked passed through her. Quickly Jennifer whipped her head around as she heard familiar voices.

"John? _JOHN!_ It's Jennifer… Rodney? You all look so young"

As more people began to enter the city, the voices faded to a low hum while once again the familiar voice spoke softly and lovingly to her.

"They can hear you Jenny, they can't see you"

Slowly she turned as a figure walked towards her and began to form into the image of her grandfather.

"Why am I here? What the hell is going on"

"This is where it all began Jennifer; this is where the humans of earth began the destiny…"

"Destiny? What are you talking about?"

"You don't understand do you?" He said with a southern accent.

"I get that a lot… I know who you appear to be… who are you?"

"Your Grandfather of course. This could take some time; I didn't want to reveal it all to you just yet. But something has changed, someone is changing the path of… the Tau'ri and that is something I can not allow"

"You mean the clone?" She laughed. "He's changing the destiny of the Tau'ri?"

"Yes. Many years ago before the death of the Asguard race… the one known as Thor told your kind '_You are the fifth race_' He was wrong, Humanity has a great destiny ahead of it. Of you continue down the path that the Clone has created it will destroy the Tau'ri"

Laughing she walked around the control room and stopped before the young John Sheppard, although she couldn't touch him, she ran her left hand over his face and smiled slightly with affection as she spoke.

"What about him?"

"He's not for you my dear… you will find no peace with him. He has his own path"

"Why am I here, Why are you here?"

"To show you the truth my dear. Remember when you where a small child, six years old. You got ill, seriously ill"

"I remember… the doctors couldn't find a cure, they told mom and dad to prepare for the worst"

"Yes. However, after six weeks… over night you got better"

"No one knows how" She laughed.

"I know, and you know. You couldn't put it all together because you where so young and feverish"

Her vision changed once again, quickly she looked around. She was in a darkened room, hanging from the roof where models of old aircraft that had been painstakingly assembled and carefully hung from the ceiling.

"Oh my god, this is…"

"Yes" He whispered. "And asleep in the bed, the little child"

"That's me?" She laughed past her tears.

"You know what to do… you remember it"

Lovingly he placed his hand on her shoulder as the young girl began to stir and look around the room. A weak voice called out as she began to sit up slowly.

"Mommy? Mommy is that you?"

"You know what to do"

Smiling slightly, she wiped away her tears and walked towards her younger self, kneeling down before her, she picked up a small stuffed toy and placed it in the girl's arms as she spoke.

"No… I'm not. You are going to be fine"

From the perspective of the young girl, she could see the woman before her almost glowing with a pale white light, rubbing her eyes she pulled her self out of bed and sat in awe at the vision before her.

"Are you an angel?"

"Yes and no… You are going to be fine Jennifer; you will grow up to be a great pilot"

"I am?" She smiled.

"Ohh yes, you are going to change the world one day. But first, you need to get some rest…"

Slowly the young girl forced a smile past her strange illness while the vision before her carefully placed her back under her covers. For a moment as she touched her arm a sense of static and a slight glow passed between them as the young girl lay in bed and placed her head on the pillow.

"You can not tell anyone about me. Not even Bobby or Grandpa. Do you understand?"

"No, but I will keep the secret" She whispered.

"I know you will. You have a great future ahead of you. You will grow up to be beautiful and strong, see and do things that others can only dream of"

"I am?"

"Yes… I promise. I have to go now, but I will be with you always Jennifer"

"No, please stay…"

"I can not; your grandfather will be here in moment. No one can see me, good bye"

Slowly she faded from the young girls view as she looked up with a bright smile for the first time in weeks.

Once again, Jennifer stood next to the image of her grandfather as she wiped the tears from her eyes.

"It was me? All the time it was me?"

"Yes, now watch" He replied with a smile.

Slowly light entered the room as the door opened and a younger version of her grandfather entered, her jaw dropped as he walked through her and stepped to the bedside and knelt down and spoke to the young child.

"Well, you look better lil' one" He smiled.

"Yes grandpa, I feel better…"

"I can tell, here… I brought your medicine"

Slowly the young girl swallowed the tablets and took a sip from a glass as she sat up and wrapped her arms around her grandfather as she whispered in his ear.

"I saw an angel"

"Really? He smiled. "What did she look like?"

"Beautiful, glowing… she said I was going to get better and be a great pilot"

"Well, I guess we'll have to teach you then"

"Really?"

Laughing he tucked her back in bed and stood up with a groan as he spoke.

"Of course, you'll have to get better first lil' one. So you get some sleep, if you see another angel, say hello to her for me"

Smiling he turned and walked towards the door, as he passed by the older Jennifer he winked at her slightly as closed the door. Shocked she turned to the image of her grandfather and spoke with disbelief.

"He… you could see me, all this time and you could see me?"

"Yes, from that day I knew that the others where wrong about you"

"What others?"

Finally, her surrounding changed once again to a large cathedral like structure; the large room was empty with the exception of Jennifer and her grandfather.

"World War Two, I was shot down over Germany…"

"Yes, I know the story"

"Not this part. I never told anyone, people believed I was captured and placed in a P.O.W camp. That's not what happened… I took a hit through the cockpit at close range, the bullet passed through both my legs and out the other side, two in my thigh and one in the chest. I was dying…"

"You ascended?"

"Yes, but not for the first time. You see my dear; I am what you would call an Ancient. We knew the Tau'ri would re-open the Stargate and eventually make contact with the Ori… in 1946 I retook human form and began a process of selective breeding…"

"_WHAT!_" She growled.

"We knew the Ori would create Adria. Some of us disagreed with the others and returned to human form in the hopes of creating our own version, you Jennifer… you are the one"

Laughing she looked at the ceiling, it appeared so far away yet close enough to touch.

"Me? I'm an Orici?"

"No… and yes"

"Are you intentionally being cryptic, or just trying to piss me off?"

"Jennifer, it is difficult to explain with his… vocal communications"

"Try!" She yelled.

"If you where to ascend… you would understand"

"No! Talk to me…"

"It was intended that you join the Airforce, be assigned to the Stargate Program… eventually you would have realised your full potential and engaged Adria on a level playing field but…"

"I went to a party at sixteen, got drunk and walked into the wrong recruiting office. I joined the Navy"

"Exactly, you where to be prepared for your eventual contact with the Orici. But now something else is happening"

"You mean Jack?"

"Yes. He is about to create an army of partially ascended clones based on a mixture of yours and his genetic makeup. He will be more powerful then Anubis if he completes his research. He has even gone further then Anubis by experimenting on himself…" Quickly he trailed off.

"What is it, grandpa… what is it?"

"The others are watching, I don't care anymore… they will not stop him until it is too late. You have to stop him Jennifer. The clone can not be allowed to complete his research"

"How? How can I stop him?"

"You will know what to do when the time comes; you have the ability within you"

With a large smile, he placed his left hand on her cheek lovingly as her surroundings began to fade.

"Wait, grandpa wait"

"You have to go now! Your people are in great danger Jennifer… you have to help them"

"What? Who?"

Images began to run through her mind at high speed, for a split second it was as if she could see what was happening all over the galaxy at the same time. Death and destruction as the fleet led by the Clone had begun to make his final move against the Lucian Alliance and eventually earth. She saw the destruction of Atlantis and earth and the death of everyone she had known and loved, until only blackness and finally she returned to where she was before the start of this long and powerful vision given too her by her grandfather.

Sounds, images and feelings began to return to her as her eyes began to open and the horrifying sound of laughter in the dark room.

"She awake, that makes it more fun I guess"

A large hand grabbed her jaw and moved her head from side to side, as her vision cleared and she looked into the laughing face of a large man stood before her.

"Welcome back… I was hoping to see those beautiful eyes… before I cut them out" He laughed.

Looking around the room, she saw strands of her hair on the floor and blood dripping from her wrists and ankles as she began to cough up blood slightly.

"Aww, comfortable I hope?" He mocked.

"For now…" She smiled darkly. "… But know this, first… I'm going to break your neck. Second, I'll use your body as a shield against the bullets from his gun, then I will take knife off your belt and stick it in his chest. After which I will take his gun and kill the rest of you, this will happen before anyone can react… so if you all have any last words, sat them now"

Laughing the large man grabbed her jaw once again and began to squeeze as he looked into her eyes and spoke.

"And how are you going to do that, when you are hung from the roof by your wrists and ankles?"

"Not for long…"

Smiling she spat her blood into his face, as he let go of her to wipe off the blood, the chains released themselves as she jumped and grabbed the large man and snapped his neck with one move. Quickly she spun him around as bullets exploded into his chest. As he dropped to the floor, she grabbed the large knife and threw it into the second man's chest before rolling and grabbing his gun. Quickly marking the remaining three targets and fired with amazing speed, as the fell to the floor dead she stood up and looked around at the dead men at her feet as she smiled and mocked them.

"I told you"

Throwing the empty gun to the floor she clenched her fists as the many cuts on her arms and wrists began to heal, smiling to herself she pulled clothes off one of the dead men and gathered as many weapons and ammunition as she could before leaving the room and sealing the door.


	8. Chapter 8

**In 2045...**

After polishing off the last of the second bottle of Whiskey, the room began to spin around them as Sheppard and Ronan laughed and spoke of both the good times and the bad times. Although their laughter held back the true feelings of what was happening inside the body of the ailing former General, the lighting in the room had been almost deactivated as a slight glow from the medical monitors barely illuminated the spot they both occupied. Shortly after the end of The Great War, Ronan Dex married a young woman he had met the year before, what shocked everyone the most was not that she was Jaffa but an artist and sculptor. A beautiful, kind and loving young woman whom he had fallen for since the first time they met. Their relationship progressed quickly as she took up residence with him within Atlantis, quickly making a name for herself in the art world as a promising and brilliant artist using his old stories as an influence in her art.

Slurring his words he struggled too his feet as he staggered out of the room.

"I… should hit the head"

"Again? Fourth time this hour Dex" Sheppard laughed.

Laughing too himself Sheppard sat alone in the dark as he sipped the last of his drink, slowly placing it on the table next to him he knocked off the bottle and laughed slightly as it smashed on the hard floor below. Taking a large deep breath, he looked up at a corner of the room and spoke aloud.

"I can't see you… but I know you're there…"

From the darkness a form began too appear with a dim glow surrounding the figure, almost as if blowing in the wind the long blonde hair and gentle and loving eyes began to appear as the figure materialised into the form of a young woman. Slowly she stepped towards him and looked over him as she smiled.

"Did you think I had forgotten about you John?"

His jaw dropped as he recognised her almost in an instant.

"Ohh my god… J-Jenna?"

"Hello old friend" She smiled.

"What? I-I…"

"Try not to speak too much… You don't have long left. That is why I am here, now"

"What, why, how?"

"I know you have lots of questions John… let me just say, you are going to complete the journey you started when you where living with those people for six months in the Pegasus Galaxy"

"What? How did you know that?"

"Ascended, remember? Thirty years ago… to you that is, I took a broken and lost puppy under my wing, I fixed his leg and sent him out into the world. Now your time has come John… come with me"

Slowly he struggled to sit up as she placed her hand on his chest, what ever she had done to him made the constant pain disappear, he felt stronger. It became easier for him to breathe as he sat up and looked around in shock; once again, his vision was clear of the fog he had lived with for so many years.

"What the hell?"

"Come with me John…" She said softly.

"What have you done to me?"

"It will not last John, but I have given you back your youth. You are as I once knew you"

Laughing to himself, he stood and walked towards the nearest mirror, once again his jaw dropped as the face looking back at him was almost unrecognisable, youthful, around thirty years old with a full thick head of black hair.

"Why?" He laughed.

"I could leave if you wish, tonight you will die painfully. I cannot let that happen to you John, I'm offering you a second chance. Come with me"

"Where are we going?"

Slowly she walked through the hospital bed and stepped to his side as she held out her hand to him and smiled, his heart began to pound faster as he reached out and took her hand. Slowly she turned into a pure white energy and enveloped him; a brilliant white light began to glow from him as he stood with a calm and soft smile on his face. His form vanished into a pure white energy as he joined with hers and began to swirl around each other as they began to move towards the ceiling. From the back room Rodney, Karen and his twin daughters saw the strange glow filled the room, almost at full sprint they ran into the room as Ronan entered from the toilet, almost in unison their jaws dropped as they saw the two unusual forms of light swirl around each other as they moved towards the ceiling and vanished from sight.

The two young women looked up at the ceiling in shock while Ronan and Rodney walked to the centre of the room and looked at each other. Laughing slightly McKay knelt down and picked up the clothes he was once wearing.

"What… What the hell was that? Where is Sheppard?" Karen said in shock.

"Where indeed" Rodney smiled. "It's a very long story Karen, I'll tell you later"

"No, _NOW_ Rodney… I want to know now"

"Lets just say… he's better off where he is, then where he was" Ronan said a with a slight laugh.

**In 2015... **

**December 24**

Sat alone on the balcony overlooking the Tau'ri city before him, John Sheppard smiled slightly as the cool breeze blew off the ocean before him, the pain in his leg from the bullet wound taken two years earlier throbbed slightly from the cold winter morning as mist drifted on the surface of the water. For the first time in over a year he felt as if a weight had been lifted off his shoulders, calmly he reached for the flask of coffee at his side and poured himself a drink into his favourite mug, a chipped and almost cracked old black ceramic mug barely holding itself together. In many ways, it was a symbol of himself, broken, battered and barely holding together. Yet it was one of the few things he could fit in his case when he first set foot on Atlantis many years earlier, it had survived attacks against the city and many years of punishment but it had always held together somehow. Content he blew the steam from the cup as he took a small sip of the strong coffee, placing the cup on the floor next too him he closed his eyes and breathed deeply.

"This, is why I come here" He whispered too himself.

As he took in yet another deep breath, he could hear the distant sound of the city's alarm bellowing out while the familiar sound of the city shield being raised around them. His eyes opened quickly as he jumped too his feet and looked around as orange and yellow bolts of energy began screaming down from the skies above and slamming into the city shield grid. He could not believe what he was seeing as in the distance energy bolts slammed into the distant city before him causing explosions and buildings to fall. Turning quickly he stepped towards the entrance of the city as something hit his foot, looking at the ground before him he saw the small black mug tumble off the balcony and smash as it hit the main tower on its long journey to the ocean below. A broken mug was the least of his worries as he ran into the control room while McKay and the rest of the command team looked on in shock at what they where seeing on the monitors.

"_REPORT!_" He yelled.

"John, we got a major problem" McKay yelled.

"You think, what the hell is going on?"

"We got a fleet of fifty ships just appeared above the planet, defence grid is on line but they are targeting Atlantis, the SGC… and any other city they can target"

"_WHAT?_" He said in disbelief.

"Confirmed, we're getting reports from all over the planet of a full scale attack on Earth. We're scrambling all 302 and Jumper squadrons"

"How many ships do we have in the area?"

"Not enough John. The Hammond, Washington and Carter engaging the fleet. But it's not enough; we're launching every ship we can get online…"

Slamming his fist against a console he looked around as calls for help began to flood into the control centre.

"Open a channel, emergency frequencies"

"Channel open John"

Taking a deep breath and looking around at his crew, he picked up a headset.

"This is General John Sheppard of the Tau'ri Installation Atlantis, to any and all ships within range of Earth. We are under attack from a large fleet of Alliance vessels. They are targeting our civilian population, we request immediate assistance. Repeat this is an emergency transmission to anyone within range of Earth, requesting assistance"

It appeared as if time stood still as he looked around his command, everyone looked at him with shock as yelled out his next order.

"Rodney… hail the orbiting fleet"

"Aye sir. You're on with the lead ship"

"This is General John Sheppard commanding Atlantis; You are targeting a civilian population of this planet. Halt your attack… I am willing too hear your terms. Respond on this frequency"

The command centre fell silent as disbelief had began to run through the large hall like room as if it was some dark spectre. Slowly McKay looked up at Sheppard and spoke the words everyone was almost afraid to say.

"What the hell are you doing John, Surrender?"

"Trust me, tell our fleet to cease fire, but hold their ground"

"John, what the hell are you doing?" He growled.

"Listen to me, the nearest ship is hours away. If we can hold them off long enough… maybe we stop anyone else dying"

"But surrender?"

"Status of the city shields. Rodney, status of the shield?"

"80% and slowly falling" He grunted.

"How long can you keep the shield active?"

"I don't know… John, I hope to god you have a back up plan, and a damned good one!"

"Trust me…"

Slowly he turned away as he looked at the large screen behind him and whispered too himself. '_So do I!_'

"John, receiving a communication from the lead ship, it's just three words… _Go to hell_"

On the bridge of the Vengeance, Major Amanda Dickens reviewed the damage delivered to the new ship by the ancient drones fired from the surface; the remaining personnel had been moved from the outer hull to the interior of the ship as emergency bulkheads had dropped to protect the ship.

"Primary shields are recharging, secondary shields stabilised at 50%, all weapons fully charged… Primary and secondary cloak at full strength… what about the engines?" She asked politely.

"All engines at 100%, luckily the damage is now contained, all vital systems in that area has been rerouted" Called out an engineer.

"Excellent, impressive ship" She said with a smile.

However, her smile was quickly broken as the communications officer almost jumped out of her seat in disbelief at what she receiving.

"Major? We got another problem. Picking up a distress signal, very weak… I've cleaned it up. I think you should hear this. On audio now"

"_This is General John Sheppard of the Tau'ri Installation Atlantis, to any and all ships within range of Earth. We are under attack from a large fleet of Alliance vessels. They are targeting our civilian population, we request immediate assistance. Repeat this is an emergency transmission to anyone within range of Earth, requesting assistance_"

The bridge fell silent as they all looked at the Major with a million questions however, all she could do was stand frozen to the spot in fear for what was happening to her home planet.

"Orders Major? Major Dickens… orders?"


	9. Chapter 9

**In 2015... **

**December 24**

Panic rang through the streets as the onslaught from orbit continued, almost every major city on the planet had taken several hits yet, some more then others. Washington D.C. was a major target for the many vessels firing at Earth, although the Earth fleet was small, it had begun to defend the planet with everything they could launch. From Starships, F-302s, Lantean and Tau'ri Designed Hybrid Jumpers even captured Goa'uld ships had been launched to take out the space faring fleet as all remaining conventional military aircraft scrambled into the air to take on any gliders that entered the atmosphere. However, word had reached the surviving military forces of alien troops on the surface in many cities. The local police forces and armed civilians where no match for the heavily armed Jaffa and alien warriors as they swept through the cities almost as if they where looking for something specific. First the ships would boots on the ground after an orbital strike, then search for what ever they where looking for, if nothing found they would launch an attack from Gliders, Al'kesh and larger ships. Yet in one town, in an insignificant corner of England, troops began to land on the ground after an orbital strike. Almost moving from building to building the large Jaffa force stepped closer to the small group gathered inside an old abandoned warehouse. As they entered, they split into small groups to search the area as hidden from view, hand signals where given to the small group hidden away, '_3... 2... 1..._'

A flash filled the warehouse as the Jaffa covered their eyes in pain, almost instantly the gathered group leapt to their feet and fired their suppressed weapons at the large force. Sparks flew off their armour as the small force of Tau'ri had expertly targeted each Jaffa with ease and efficiency of many years of military training. As the last Jaffa fell, the leader of the group walked around his cover as his team shot any Jaffa still moving, nodding to his second he spoke with a cool and calm voice of many years experience fighting the Jaffa.

"Let's do it. Grab the controller and their weapons, vaporise the bodies before someone comes looking for them"

"Sir?" His second said with shock.

"If anyone finds these bodies, we're screwed. Go bring the prisoners… the rest of you secure the area"

"Yes sir, then what?"

"Then my dear, then we wait for an Al'kesh, we ring aboard and take the ship"

"It's that easy?" She laughed.

"That is the easy part. The hard part is getting the prisoners to Atlantis without being shot down by either side. We'd be in an unregistered vessel, our ships wouldn't recognise us with friend of foe systems, and once those ships find out what we've done, they'll hunt us down"

His almost two decades long experience in fighting the Jaffa was about to pay off as a large vessel hovered above the building, on the ground the spent bullet shells begun to vibrate as dust kicked up into the air while he looked at he room and smiled. Nodding too his team they stepped close too him with weapons drawn as the prisoners stepped into the centre of the circle, slowly he lifted up the control manacle for the Goa'uld ring system, as the rings dropped around them, they vanished in a halo of white light as the building collapsed in the space they once occupied.

Pain began to rip through her chest as she focused on the mission at hand, freeing her landing team and wither destroying the ship or capturing the vessel however, one thing was clear, the clone would not survive and the research had to be destroyed. Although her pain receptors had been shut down, this pain burned like a star within her, for a moment she fell into an empty room and clenched her chest, she felt as if her heart was about to explode. Focusing on the moment, she clenched her eyes shut as the pain began to subside slowly until it completely vanished, but now something was different. She felt a new clarity within her mind. '_Is this what death feels like?_' She asked herself, squeezing her weapons she looked around the door and smiled slightly as she could see they way ahead was clear.

Covering the distance to the holding cells where her team had been held was not difficult, although as she looked around the corner slowly, she could see four large guards standing before a large Lantean designed holding cell. The design appeared to be almost identical to those on Atlantis; slowly she moved her head back into cover as she thought quickly. Once again, she slowly peered around the corner as Ronan looked up slowly. His face was stoic as ever, until he ran his fingers through his hair, nodding softly she moved back into cover.

"Great he saw me, now what? With possibly four more guards around the far corner"

Carefully, as not to make a sound, she checked the ammunition on her weapons. Each magazine was fully loaded, yet now something happened. Her right hand reached out, as if acting on its own, and touched the wall panel. Taking a deep breath, she closed her eyes as a feeling ran though her, a feeling of static electricity and now something different, she could almost see what was happening inside the holding cell itself. Once more pain ran through her, yet this time it was her mind that was burning like a hot flame. Her vision moved around the room as she seemed to check each person within the holding cell until finally her hand whipped away from the wall panel as each person inside was safe and unharmed but for the effects of whatever had stunned them earlier.

Her mind began to race as she looked around her immediate area for anything she could use to distract the guards from their post, however one thing was clear the guards where human, not Jaffa which would make what she had to do next easier. Carefully she attacked silencers too the two weapons she took from her captures, weapons of Tau'ri design obviously taken from the mission team, cautiously she leaned around the corner and took aim at the first two guards and fired one shot at each guard. As their heads exploded from the supersonic impact from the bullet she re-aimed her weapons in an instant and fired two more shots, quickly she covered the distance to the holding cell door and targeted the reaming guards stood at the end of the hall and once again fired one shot into each of the guards, as they fell backwards she stood and smiled slightly as she deactivated the forcefeild holding the prisoners.

Smiling Ronan entered as she handed him one of her weapons, looking around he replied with a half smile.

"I'm glad you're on our side Cole, are you okay? We thought you where dead"

"I'm not fine… but I'll live. We have to stop this ship from taking off"

"Agreed… Barrett and Williams take your teams and secure the Engine Room…"

"No, get down to auxiliary control and reroute all primary systems to the Drone Chair. Helm, sensors, navigation the whole damned thing… then lock it down. If this ship gets airborne, they will use it to attack Atlantis. I'll head upto the bridge and attempt to take over from there; if not… we'll destroy the ship. Ronan, contact the Vengeance and have them target this ship from orbit. If we can't commandeer the ship, I want nothing but a smoking crater, then get everyone off this ship and get back to the Jumpers…"

"What about you?" Ronan sighed.

"I have a personal score to settle, I'll be fine… trust me. Go…"

Nodding slightly he stepped back as he looked at his large team, as they picked up the weapons from the bodies she began to walk away from the experienced teams. Turning slowly she smiled at Ronan, for some reason he had a feeling it would be the last time he would see her but as a seasoned warrior he had to burry his feelings and attempt to move past them.

"Cole, be careful"

"Always am!" She with a wink.

Laughing to himself slightly, he turned in the opposite direction and followed his team away from the holding cells as she disappeared around the corner.

**In 2045...**

The mysterious disappearance of John Sheppard had echoed around the home planet of the Tau'ri, as conspiracy theories had taken hold like wild fire around the planet. Some of the more outlandish theories claimed that he had been rescued from the brink of death by survivors of the Asguard race discovered in the Pegasus galaxy many years ago while others claim he had placed in stasis until a cure could be found for the mysterious illness he had contracted many years ago. However, those who knew the truth about his disappearance had been sworn to secrecy, as Ascension had become a closely guarded secret known only to the highest-ranking officials in the combined military.

Slowly and with a sombre feeling hanging over him like a dark cloud, the Vise-President stood at the podium before the large Atlantis Stargate, to the left and right of the Stargate the flag of the Tau'ri swayed in the breeze caused by the open doors as the afternoon breeze blew off the ocean that surrounded the city as two flames burned near the Stargate.

A large crowd had gathered in the gate room as news cameras focused on the large Tau'ri male as he cleared his throat and began to speak.

"Thank you all for coming; as you are aware… this press conference will not be attended by President McKay and his family due to the untimely death of Former General John Sheppard. As I stand here in the Gateroom of the great city of Atlantis, I stand on the many worlds that make up the Great Alliance of the Three Galaxies…"

Laughing slightly he straightened his jacket and as he thought for a moment.

"… For the first time in the history of this world, we are free from violence, poverty, hunger and war and in it due to those who where charged with the incredible and often terrifying task of protecting this world from threats that existed outside this solar system. Over fifty years ago a small team led by Colonel Jack O'Neill stepped through the Stargate for the first time and encountered a new race on a distant planet, little did he know that moment would set the human race as we knew it on a collision course with history, many years later a team led by Doctor Elizabeth Weir discovered this great city in which I now stand. A team consisting of Doctor Rodney McKay and the then Major John Sheppard. Although that brave team presumed lost for a year in a distant galaxy made some friends, they also made powerful enemies some of which we now know as the extinct species… the Wraith. Yet upon the return to Earth, this great city became the centre of a great war that almost devastated this planet. In a cowardly attack by a great force then known as the Lucian Alliance cost the lives of 19 Million civilians and military personnel on this world alone, but we fought back. Since that vicious attack on our home planet we fought back… although the war did not come to an end on this day, we count this day as the day the Tau'ri united under one flag and one purpose. It was the day the Tau'ri stood up with one voice and declared that we will not go silently into the night. We will fight to the last man and woman, we will fire every gun, use every blade and when we have fired every bullet and launched every bomb and rocket, we will use sticks and rocks to defend ourselves and our planet.

Applause exploded within the control room as the Vise-President bowed his head slightly before he continued with his speech.

"…Today is a day we will make in history. Under the authorisation of the President and the High Council of the Tau'ri… All files of the Stargate Program will be made publicly available in a new library specifically designed for this purpose, we no longer be known as Human or Tau'ri this planet will no longer be known as Earth… we are the Guardians of the Lantean and Asguard legacies. We are… The FIFTH RACE!"

Applause once again ripped through the great city as above the city fireworks exploded in a multitude of colours and formations as the latest designed star fighters screamed above the city, smiling too himself the Vise-President stepped down from the podium as reporters ran towards him with a million questions.

"Mister Vise-President… What do you mean by we are the fifth race?" One reporter yelled out.

"Once all the files are made public, it will all come clear" He laughed slightly.

From the far corner of the room a voice called out as an old man entered the room, shock rang through everyone as the face was instantly recognised as the many reporters ran towards him yelling his name. Quickly he pushed past the reporters and stepped up to the podium with a slight smile on his face.

"I'm sure you all know who I am, many of you probably have thousands of questions, I will take two and only two"

Seizing an opportunity, the Vice-President stepped to the old man's side and spoke as he placed his arm around the man before him.

"Today is a great day, today marks the return of one of the greatest warriors known to humanity… Master Teal'c of Chulak!"

Quickly a reporter yelled as she pushed her way towards the front of the gathering large crowd.

"Master Teal'c, Master Teal'c… Last reports claim you died during the Battle of the Line. Where have you been the last thirty years?"

Silence fell over the large room as he smiled and bowed slightly before he spoke.

"After the Battle of the line as you call it, I immersed my self in a Jaffa ritual. I believed that exile would further my immersion. I was a different person before, angry, bitter, and betrayed by one who was close to me. I placed my son Rya'c in my place with the High Council of the Jaffa and Tau'ri, he was sworn to secrecy… my location known only to him and his wife, with his approval I have returned to my rightful position and declare his candidacy for the next election as President of this Great Alliance"

For the first time since the creation of the Great Alliance, an Off-worlder as they had come to be known had declared interest in running the vast Alliance. Jaws dropped as the Vise-President turned to face the old and deadly warrior at his side as Teal'c turned with a dark smile and looked at him.

"Prior to this announcement I had spoken with the President whom has informed me that next year he will stand down as President, he has also given his personal approval of Rya'c's candidacy and he will stand at his side during the campaign"

"Master Teal'c, Master Teal'c… why this sudden move in politics? Who will stand as his Vise-President?"

Laughing slightly, Teal'c leaned closer to the microphone as he replied.

"Standing at his side will be a man you will all come to know in the year ahead, the son of John Sheppard from his second marriage… Jonathon Marshall Sheppard Junior"

Little was known about the man, even his name had been hidden from the public, however, to those who knew him he was a strong and dedicated career military officer who had served with distinction and honour in the Tau'ri force. Baring an almost eerie similarity to his father with the exception of short cropped brown hair and a neatly trimmed beard, his middle name was given to him in honour of the Military officer during the first days of the Atlantis expedition Colonel Marshal Sumner killed by Sheppard himself as he was interrogated by a Wraith queen during a rescue mission in the Pegasus Galaxy.

Almost laughing, Teal'c stepped down from the podium and walked towards the gathered crowd as they ran towards him. Smiling to himself, he pushed past the many reporters and distinguished guests, turning only slightly to look at the expression on the Vise-President's face one of shock and betrayal.


	10. Chapter 10

**In 2015... **

**December 24**

Devastation rained down all over the planet as the Lucian Alliance and its Jaffa Allies continued the campaign of orbital bombardment of Earth, the foul stench of death and burning flesh covered every city as civilians hid in the subway systems of many cities while the overwhelmed military and police forces attempted to control the situation. Friends and enemies alike put aside their differences and stood shoulder to shoulder as they defended the planet against the deadly onslaught from orbit. Many of the civilians who owned weapons stood at the side of those highly trained officers from all branches of military and civilian defence, united with the common goal of protecting those who where unable to fight. For the first time in human history, every man, woman and child of every race and religion stood side by side in defiance and defence of this once isolated and insignificant world on the rim of the galaxy.

Overwhelmed by the vast enemy fleet before them the small Tau'ri fleet of starships, fighters, Goa'uld designed bombers and cruisers continued to press forward the attack against the enemy fleet while the satellite defence network continued to launch everything it was capable of at the enemy fleet, yet it still was not enough as more enemy ships arrived in orbit to continue the bombardment. Almost every friendly vessel within range of Earth slowly began too arrive in defence of the planet while on the city of Atlantis all the crew could do was direct the battle above the planet and watch helplessly as millions of civilians died. Above the city Goa'uld designed gliders attacked the city shields as Tau'ri F-302s and conventional aircraft attempted to direct the fire away from the valuable city.

"John, shields are down to 20%, we can not hold this for much longer" McKay yelled. "We should evacuate the city"

"And go where?" He barked. "Defence teams, concentrate all firepower on the lead gliders, we have to break their formation"

"Aye sir" Called out the communications officer.

"Sir, the Washington's shields are failing, the Carter is moving too assist"

"Negative, order the Carter and Hammond to focus all firepower on the Flagship, Jaffa vessels five and nine take up the Washington's position, allow them to withdraw and recharge shields" Sheppard yelled.

Explosions ripped through the city as holes began to form in the protective bubble as firepower from orbit and the attacking Gliders began to hit home on the great city itself.

"Sheppard, shields are failing!"

"Defence teams Alpha and Gamma, cover those holes. Squadrons Eight and Twelve protect those areas NOW!"

Streams of energy flowed from the great city as its crew defended it to the best of each man's ability, above the planet the vicious battle continued as the hopelessly outnumbered vessels and defence grid gave everything to defend the planet below, as more enemy ships arrived to continue the battle, the Tau'ri and loyal Jaffa fleet became more hopelessly outnumbered as they attempted to make a hole in the vast enemy fleet. The battle was destined to become one of legend as each aircraft, fighter, starship and Tau'ri on fought against the Lucian Alliance. However, with each Starship destroyed it appeared as if another two had arrived to take the fallen vessel's position. Once great and powerful nations and cities began to fall to the vicious attack from orbit, as the worst fears of the Stargate Program had become a terrifying reality, an orbital attack against Earth itself.

The layout of the ancient warship was unfamiliar, although each system was similar to those on Atlantis yet, more advanced. Slowly moving through the ship Cole kept her weapon trained before her as she moved through the ship towards what appeared to be the command centre. With each person that came before her she fired a single deadly shot, ducking into a dark corner only to reload her weapon until finally she entered the bridge. Marking the position of each person in the bridge she rolled too her left and fired single shots at each of the ships crew before her until she stood face to face with the young man who she had been hunting since her release from captivity. Smiling she stood as the last man fell, the red dot from her half loaded P90 beamed between his eyes as he stood clapping his hands in applause at her entrance.

"Well done Miss Cole, I never thought you had the balls for that. You've saved me a lot of money"

"That's what this… all this is about, Money?" She yelled.

"How small you are. But I must say, I rather enjoyed you without those clothes on" He laughed. "Take them off my dear; show me what you have for me?"

"Over my dead body!" She barked.

With almost lightening reflexes he reached behind his back and drew a large weapon, smiling too herself she stepped over a body as they circled each other slowly.

"Ronan's gun… nice. I've been looking for that. Recognise this?"

Quickly she a side arm before his eyes as he looked on in shock at what he saw.

"Yeah… ohh don't tell me you don't recognise this. You have no idea how much paper work it took me to get this"

His eyes clenched with pain as she flashed the gun before him, for an instant, he lowered his weapon. Seeing an opportunity, she stepped forward but not before he regained his senses as aimed his weapon once again.

"Where did you get that?"

"Storage. You'd be surprised what the SGC keeps on file. This is Jack O'Neill's gun… the one that…"

"Charlie shot himself with. Charlie… my son… why?" He yelled.

"He wasn't your son; you're a clone Jack… a pretender to the legacy of Jack O'Neill. Jack O'Neill would never start this war, the blood of millions are on your hands. I got word before I left… Sarah O'Neill was killed while cruising on the Golden Gate Bridge when the Achilles crashed into the bridge… ordered by you Jack. You killed her…"

"… No, no it's not possible. She was in Wisconsin" He screamed.

"No Jack, she was coming to the Bay area to see Atlantis and visit with friends. You killed her Jack, you killed Sarah"

Slowly and carefully, she made her way past the bodies and stepped closer to him. It was almost as if her words echoed in his mind as she stepped closer too him and handed him the gun.

"Take the gun Jack, take the gun and finish it before more innocents die, more innocents like Sarah and Charlie" She whispered.

Slowly his left hand reached out and grabbed the gun, carefully he examined the weapon and smiled slightly as he aimed at Cole and laughed.

"I see you have come to realise what you truly are my dear. But you do not know what I am!"

Slowly he turned the gun on her and pulled the trigger; with a dark smile on her face, she pulled the gun from his hand as she spoke.

"Do you think I'm stupid Jack, Giving you a loaded gun… you want me? Come and get me"

"You balls babe, I'll give you that" He laughed.

"_NEVER CALL ME BABE!_" She yelled.

In the blink of an eye he pushed forward, it was as if she was hit by a heavy weight as she flew over the nearest console and crashed down onto the ground behind her, smiling contently Jack walked towards her and aimed the large alien weapon at her head. Reacting in an instant she swept his legs from under him and flipped too her feet before he hit the floor hard.

"Goody, a challenge" He mocked.

"Why don't you put the gun down, Come on Jack… Stick a knife in me!"

Smiling she placed her P90 on the command chair behind her as she pulled a large military style knife from her belt line.

"Come on Jacky Boy… Let me see that badass training you… or should I say Jack O'Neill is so famous for"

"_I AM JACK O'NEILL!_" He yelled.

"No Jack, you're a coward…you're nothing but a frightened little boy hiding behind big guns and big spaceships. If you can't kill me, what can you do?… Bitch!" She laughed.

Anger burned within him as he jumped too his feet and grabbed a Jaffa style blade off his belt and passed it between both of his hands as they circled each other. With a smile on her face, she flipped the knife over so the blade was facing in a downward position towards the floor, lunging towards her he swept at her with his blade. The sound of steel on steel echoed through the bridge while each of his strikes was deflected by her expert hand, laughing like a mad man he moved backwards one-step as he assessed her movements quickly.

With a slight smile on her face, she took off her jacket and through it onto the floor nearby; as he stepped towards her once more, she kept her blade moving in a constant and fluid movement. Quickly she grabbed his hand and threw him to the ground hard.

"Amateur!" She laughed.

"No, I'm just getting started" He growled.

Smiling darkly, he pulled a small blade out his boot as he stood slowly.

"Enough foreplay babe. I offer you a choice; give yourself to me… your mind, your abilities and your body. I will let you live, if you do not… one of us will not leave this ship alive"

"Go screw your self…"

"As you wish" He laughed.

Quickly he stepped towards the nearest console and activated a control; the whole ship appeared to vibrate as a loud hum echoed through the ship. Anything that was not secured began to slide around slightly as the sound of the ship's engines growled into life.

"What did you just do?" She screamed.

"Activated the engines of this amazing vessel"

"_SHUT IT DOWN_"

"Umm… nope…" He mocked. "It can not be stopped until it reaches its destination, Earth"

"Earth, Why?"

"Many hours ago, under my orders a large Alliance fleet exited hyper-space above Earth with the instructions to exterminate all life on that little planet. Once it is a dead world I can begin my true destiny…"

"_WHAT?_" She growled.

"Ohh yes, your little ship in orbit. It's an impressive vessel Miss Cole. A pity I have to destroy it, it would have made an excellent trophy"

Practically all of the command functions had been rerouted into the chair room, however, they where too late. The large engines had begun to activate and slowly the ship had started to become airborne, with all concerns now second, the large team led by Colonel Dex followed the last orders given to them, orders to evacuate the ship. Quickly the covered ground until they reached the airlock they had entered the ship while the vessel began to climb.

"I see no choice Colonel, we have to jump"

"Agreed. GO!" Dex Yelled. "Get to the Jumpers"

As the ship began to climb into the air, they jumped out of the vessel and landed on the hard ground below, the last one to leave was the Colonel himself. As he hit the ground, a loud crack was heard as rolled on the floor in pain.

"Colonel?"

"My leg, I think it's broken" Yelled in pain.

Carefully two of his team helped him too his feet as they moved towards the two jumpers, carefully they placed him in one of the seats as both the twin jumpers became airborne.

"What about Cole?"

"She's on her own now… target the engines of that ship… maybe we can cripple it before she gets into open space"

The two sleek black jumpers appeared behind the large vessel as their weapons launched a powerful attack against the large engine ports of the ancient vessel.

"We're not making enough damage; weapons are bouncing off the hull"

"Sir, picking up a large energy reading from the ship… It's opening a hyperspace window"

A large vortex of energy appeared before the ship as it disappeared before them, screaming with defeat Ronan looked up at the consoles before him as he called out his next order.

"Set course for the Vengeance… once aboard, tell them to set course for Earth. I have a very bad feeling"

**In 2015... **

**December 25**

Dawn broke over the city of Atlantis however, for a Christmas day it brought nothing but death and destruction as it's exhausted crew continued to defend against the vicious and deadly attack that seemed to have no end, it appeared as if every ship under the renegade clone's command had appeared over Earth to continued the deadly attack. Not a single city, town or village on the face of the earth had been spared the terrifying attack, but one single hope for the survival of the Tau'ri as a race had begun too arise, every surviving Tau'ri had picked up any weapon they could find including weapons taken from the many dead that littered every street, as they stood side by side in defiance. Guns, Zats, Staffs even swords, knifes and rocks had armed every Tau'ri on the planet as they defended their homes and each other. Once sworn, blood enemies now stood holding the same patch of ground as they adapted to the alien weapons they had recovered. Yet, the main target of the armada above the planet was Atlantis itself. Its vital shields begun to fail as many of the once great towers of the city had begun to collapse from the overwhelming onslaught. The main tower of the city had begun to show signs of stress as cracks appeared in the once smooth walls as console had exploded and the foul stench of death lingered in the control tower. The last explosion that had ripped through the control centre had all but destroyed every vital system causing an evacuation of the control room itself, relegated to a backup centre set up during the Wraith war, the surviving and exhausted command staff stood shell shocked as they looked over what remained of the once proud and great city.

Bandaged and patched up, Lieutenant Colonel Rodney McKay sat at what was one of the last working systems as he ignored his own injuries and orders to report to the infirmary, he frantically worked to bring any systems back online while blood began to soak through the makeshift bandage on his leg.

"Rodney… I know you are not going to leave… what can you get up and running?"

"I can get external sensors back up… for how long I don't know. Shields are at 5.2% and falling, defence teams are running out of ammo, we simply can not hold this ground any longer"

"I can see that. Status of the city?"

"Damage report states we've lost almost 45% of the city. John we need a god damned miracle!"

"I can see that"

"Sir… getting reports of Ha'tak class ships landing all over the planet. Wait a minute… picking up an Al'kesh approaching… sir it' attacking Gliders in its path" A young woman reported.

"John, getting an audio message, we can barely pick it up"

"On speakers" He orders.

Crackling through the speakers a familiar voice was barely audible while McKay worked to clean up the message.

"… Repeat this Daniel Jackson onboard the Al'kesh. I have the package, requesting landing permission"

"Jackson? Good too hear a friendly voice. Granted, we're in aux control… get up here as soon as you can"

"On my way. Jackson out"

Smiling slightly McKay looked up Sheppard as spoke with a laugh.

"It's Christmas Theo; it's the time for miracles"

"Die Hard… nice quote" McKay laughed.

Metal clashed against metal as the deadly fight between the clone and Cole had continued, her anger had almost begun to cloud her judgement as his blade made contact with her clothing and slicing through to her flesh. Stepping back slightly she attempted to focus her mind as she circled him once more.

"This is fun… Come on Cole, put down the blade and join me. You cannot imagine what we could do together. Bring that lovely tight little ass over here"

"I would rather die" He growled.

"No, I have plans for you sweetheart"

Smiling she stepped placed her blade on a large console as she stepped around it.

"What about your wife Jack? She's cute… can you imagine what they would do too her in prison? As for your son… well. I'm sure he'll be given a nice home in five or six years that is"

"I know what your doing Cole, it won't work"

"Ohh, it already has kid. Assuming they survived your attack on Earth"

Quickly he reached out and grabbed her as she laughed slightly and pushed him away. Throwing his blades away, he threw a punch at her that was easily deflected, continuing his attack she blocked and dodged him with ease as taunted him with each attack he made. As he threw one more punch she grabbed his right arm and turned into his attack while ploughing her elbow hard into his stomach, releasing his arm she spun around once more and punched him hard in his face as she whipped her leg around for a powerful kick into his jaw line, knocking him off his feet and sending him crashing to the ground. Once again he laughed as he stood and spoke aloud.

"Ohh baby you've got skills. I bet you're amazing in bed, but I regret I will have to kill you now"

In an instant he ran towards her, smiling slightly she grabbed his arm once again and threw him into a console near by, hitting the console hard he bounced off and fell to the ground as she walked towards him and pulled him too his feet. Pulling his ear close too her mouth she whispered quietly.

"You'll never know"

Twisting around him, she once again threw him into another console as blood exploded onto the console while his nose burst, shaking slightly he stood and ran towards her. For a second time seemed to stand still as he jumped and spun around in mid air while his right foot slamming into her jaw sending her crashing to the ground hard. Whipping around in mid air, he landed wit his legs spread above her as he laughed manically and spat blood onto the floor next to her. Cole could not have foreseen what happened next as a tightness began to grip her throat as she lifted off the floor, gasping for air closed her eyes and pushed forward with everything she had. A loud crack rang out around them as Jack flew backwards and impacted the far wall as she dropped to the ground coughing and gasping for air. Almost in unison, they both stood with deadly intent in their eyes, wiping the blood from his mouth Jack walked towards her slowly as she stood her ground. Inside her mind, it was as if a voice rang out, a calm soothing voice that made her relax slightly. _'This is it little one, end it'_

Quickly she covered the distance between them as he threw a powerful punch at her, her body reacted on the purest of instinct as she grabbed his hand and twisted it fast until a loud crunch echoed around her yet, she did not let up her vicious attack on the war criminal before her. Slamming her free hand into his chest two more loud cracks rang out as he gasped for breath while she kicked at his right knee and broke it in an instant. Releasing him from her grip, she spun around and kicked hard at his jaw causing it to break, gasping for air lashed out as she spun around while a small knife whipped out of his sleeve and ploughed into her back as he fell to the floor gasping for breath. Ignoring the searing in her back she stepped over him and picked up his head, smiling slightly she whispered '_Good night'_ as she twisted his head breaking his neck and allowing his lifeless body to fall to the ground before her while the voice once again whispered into her mind. '_Duende, a part of the dance when exhaustion is taken over by the purest of instinct_'

Screaming in pain, she fell to the floor as blood poured from the knife in her back, yet the least of her problems was the blade. The large and deadly vessel was on course to join the large fleet orbiting Earth, with a full compliment of drones onboard earth would be destroyed.

While pain ripped through her body she pulled out the knife and began to crawl through the ship while avoiding the small crew onboard, hopefully she would reach the chair device before her body had given out and death took over.


	11. Chapter 11 (Final Chapter)

Explosions ripped through the great city as the Al'kesh touched down and it's crew left he vessel and entered the heavily damaged city while above, the battle raged on. With every Alliance ship firing down on the planet, every Tau'ri and allied vessels had entered the fight as an epic battle had begun to unfold above the planet, debris had made it almost impossible for any ship to move as the gravity well of the planet had begun to pull the debris in a broken and battered thin ring around the planet while the defence grid and every ship attempted to control the situation, it almost appeared as if every Starship in the galaxy had entered earth orbit to fight for one side or the other.

Quickly Jackson and his small team made their way through the city until they reached the Auxiliary control room.

"I leave for a year or two, and you redecorate this place" He laughed.

"Funny, I've always said you're a funny guy Jackson. Didn't I say that McKay, Didn't I say last week that Jackson is a funny guy?" Sheppard laughed.

"Where's the package?" McKay barked in pain.

Turning slightly, Jackson waved over his group, as they separated a young woman stepped before the General holding a young male child.

"Perfect, a pleasure to see you again Gemma. You're aware of the situation?"

"Kinda hard to miss" She grunted.

"Another comedian… damn we're lucky. Contact those ships in orbit, order them to stand down…_NOW!_"

"I'll try, but do me one favour?"

"You are in no position to ask for favours Miss"

"All I ask is that you let me and my child go, allow us too live our lives in peace. I'll help out anyway I can… I'm tired of running and hiding General. Let me give my son a home"

"I'll consider it" He growled. "Call those ships off"

Nodding slowly, she handed her son to Jackson as she stepped towards a console and activated the microphone.

"This is Gemma, to all Alliance ships above this world. Stand down your attack, Authorisation Alpha, Sigma, Omega, 394875 Code: Red, Theta"

Finally, back onboard the Vengeance, Colonel Ronan Dex limped his way back towards the bridge of the vessel whilst it disappeared into hyperspace at full emergency power. Slowly and carefully, he sat down in the command chair as Major Dickens walked towards him holding a computer tablet with a look of shock on her face that was echoed by everyone on the bridge.

"Report" He said quietly.

"We are being followed by Jaffa ships that have agreed to join us… Master Teal'c is commanding. However, we intercepted an emergency call from Earth; they are under attack from superior forces and requesting all available ships to assist. We're giving the engines everything we can to get back… but I fear we may be too late. All transmissions from earth have stopped"

"I knew it. Evacuate all none essential areas, deactivate every system and shunt the power into the main engines"

"Already done sir. Where is Commander Cole?"

Slowly and with a look of concern on his face, Ronan looked up at the Major as he replied with a cold look in his eyes.

"She decided to remain on the ship… unfinished business"

"I see, what happened down there?" She said with concern.

"You don't want to know Major"

Pain ripped through her body as she crawled the vast distance to the ancient chair, her lower body had become soaked from the blood that poured out of the wound on her back. With every ounce of strength she possessed, she reached the chair and climbed into it as she screamed in pain. The instant her body touched the sensors on the chair it activated as it tinted backwards and turned to the left while she sighed with relief. Finally she was sat down, her body was exhausted, her mind racing as she attempted to focus with all her abilities on keeping the pain away for just one more second. In her mind, a display of all the key systems of the ship appeared in a holographic display before her eyes, course, speed, sensor and weapons status. It appeared as if the ship was set on a pre-programmed course to Earth and set to target Atlantis, the Defence Grid and every Tau'ri ship and Jaffa ship on orbit. Once all resistance was eliminated, the remaining weapons would be turned on the civilian population to eliminate any sign of resistance. Focusing her mind, she was able to alter the parameters as the ship screamed through hyperspace towards her homeworld. It felt as if her life was draining away as the sensor readings caught her attention.

"Ships are tailing us at extreme range; one is closing fast… the Vengeance?" She said too herself.

Hours past, as she sat in the chair while the remaining crew of the ship attempted to break past the shield she erected around the chair room for protection. Finally the ship exited hyperspace above earth, from orbit vast fires could be seen burning on the all over the planet below, debris from Alliance, Tau'ri and Jaffa ships encircled the planet as slowly a small ring system had begun to form around the planet. Several large Alliance ships had begun to form up around the Ancient Dreadnought while it moved into position. '_NOW_' She thought, every weapons system on the large vessel fired as Drones began to scream out of the ship and target every Alliance vessel in orbit. Her heart began too slow as she focused on the task at hand while Tau'ri and Jaffa vessels alike began to form up around the Ancient ship until finally in one show of force, she launched all the remaining drones against a large Goa'uld Flagship that hung motionless in orbit.

Like the smaller ships in orbit the shields where useless as explosions ripped through the ship and finally in one huge blast and shock wave, the Flagship exploded sending debris in all directions. Shocked in awe at what where all seeing, a loud applause filled the auxiliary control room of Atlantis as McKay jumped too his feet, ignoring his pain as he screamed aloud.

"_HOLY SHIT! IT'S ONE OF OURS!_"

"Are you sure?" Sheppard sighed.

"Either that, or its weapons officer is a complete Moron… all remaining enemy vessels are retreating. It's over" He laughed.

"For now" Sheppard sighed.

Almost brought too tears, Sheppard sat in the nearest chair as he laughed past his tears as McKay continued.

"The… umm… Ancient ship is dead in space sir, picking up a transmission. It's Ronan, he's got a small Jaffa fleet behind him, they're changing course too intercept the retreating vessels"

"How many ships survived?" Sheppard called out.

"We got eighteen ships, a further twelve are heavily damaged and six are loosing life support"

"Alright, send two of the surviving ships to board the Ancient ship… find out what is going on and where the hell it came from"

"Dispatching them now sir" The young officer sighed. "Sir the Carter and Arizona are responding and moving into position"

In the following days, every available ship had begun to search for the remaining enemy vessels,

While the large task of cleaning up Earth orbit had begun as on the planet below every able-bodied man and woman had begun to round up the enemy soldiers. For the first time in years, the tired General had sat what remained of his quarters, which he had turned into an office until the Central Tower and had been repaired, voices called out one at a time as he almost appeared to be in a world of his own.

"John, are you listening?"

Quickly he snapped back to reality as McKay threw a piece of paper that he had made into a ball.

"Sorry, I was just thinking… what where you saying?"

"I said, casualty lists keep coming in, so far the list stands at 15 million dead… it is expected to climb past 20 million"

"I see, anything else?" He whispered.

"Karen has completed the autopsy of the body found on the bridge of the Ancient Dreadnought, it is now confirmed… it was the Clone. His skull was fractured in many places, his nose and neck was broken, his arm was twisted with such force it snapped, his knee and leg was broken as suspected"

"Ouch! Got what he deserved" He smiled.

"Not finished. He suffered three broken rips, a punctured lung and massive internal bleeding"

"My god, must have been one hell of a fight"

"Karen has also completed her analysis of the large trail of blood they found. It was Colonel Cole's blood, she must have crawled to the chair device and took over the ship as Ronan's report stated. The blood on the chair indicated a massive wound too her back…"

"However?" He laughed.

"However, her body has yet to be found. Considering how much blood she lost… I doubt she would have survived. I'm sorry John"

Slowly Sheppard looked through the large hole in his wall and smiled slightly as he spoke low and slow.

"I've got a feeling we've not seen the last of Miss Cole… thank you Rodney. Go home, get some rest"

"I'm fine Sheppard" He grunted.

"That's an order. Go home, spend time with Karen"

"That's something else I want to speak to you about" He smiled.

"Ohh?"

"We spoke earlier about a few things and we've agreed. We want you too perform the marriage ceremony, as Commander of Atlantis and a close personal friend"

"I'd be honoured" He smiled.

The Great Tau'ri War last a further six months after the death of the Clone, yet this time, with the loss of its greatest commander. The Alliance he had formed began to crumble almost right away once the news had been broken as the Tau'ri became stronger and formed greater Alliances with the newly re-established Jaffa Nation, a whole new class of ship had been launched based on the Lantean Dreadnought delivered to Earth. Although official records stated it was discovered by a special operations team and returned too earth, the unofficial record reports the ship was stolen from the enemy Alliance by Colonel Cole and returned to earth in an attempt to assist with the defence of the planet.

On January 6th at 0900 hours, the wedding of Dr. M.R. McKay and his fiancée was conducted by General John Sheppard on the only remaining pier of Atlantis, over looking the ocean while overhead a squadron of the latest F-302-D class aircraft flew with the '_Missing Man Formation_' as requested by the married couple themselves. Yet behind the formation of aircraft a single Mk:Vb Supermarine Spitfire flew low and slow as it dipped it's wings in respect for the one who had restored it.

Night time came as the happy couple had been sent to a private island for a honeymoon, for the first time years, Sheppard lay on his bed and closed his eyes, almost without hesitation the long since lost feeling of sleep crept over him like a warm and soft breeze.

"John, John… wake up" A soft voice called out.

His eyes opened as the voice called out once more, although the lighting in his quarters had yet to be repaired, light from a full moon beamed in through the large hole in the wall as it was protected by a small forcefeild.

"John… wake up" The voice called out once more.

Slowly he raised his head and looked around the room as in the far corner a figure appeared slowly, long flowing blonde hair, pale skin and an almost see-through dress began to step towards him.

"What? Who?" He asked.

"Don't worry John, its okay. Everything will be okay"

His eyes strained as the face began too come clear to him, sitting up quickly he smiled as he spoke.

"Cole, Jennifer? What are you doing?"

"Seeing an old friend"

"I take it the ship was your doing?"

"Yes, and more. It's a long story John, a very long story… all of it"

"I know some of it, we where able to recover data from the Ancient ship. I know what the Clone did too you" He sighed softly.

"And that is why I killed him"

"Where have you been all this…"

"Close by… yet beyond sight. I can't explain it… The others are watching, I don't have much time"

"Others? What are you talking about?" He barked.

"Never ask a question, with a question John. Because of what happened, they have allowed me to speak to you once more, and give you a gift John, a great gift"

Slowly he stood and walked towards her, almost the instant he tried to touch her, his hand past through her form.

"You ascended?… Now it makes sense"

"I have more John, in the database of the Dreadnought; you will find a list of planets untouched by anyone for thousands of years. They have enough drones and zero-point-modules combined to restock Atlantis and as many ships as needed, plans, schematics and diagrams for things you can not even begin to imagine"

"I can imagine quite a lot" He laughed.

"I know you can. Just one thing John, never tell anyone where you got your information from"

Smiling he sat down on his bed as she looked around the room once more.

"I see you have cleaned up since I was last here" She said with a smile. "Tell my father I love him John… I will see you soon"

In an instant she disappeared leaving him alone in his quarters with a slight smile on his face, quickly he jumped too his feet and dressed before running to the Auxiliary control room. As he entered, Ronan and Zelenka looked at him in shock as he walked towards them.

"What? You look like you've seen a ghost" He laughed.

"Are you okay John? I mean are you feeling okay?"

"Fine Ronan, why?"

"Where is your cane?" He asked slowly.

For a moment he looked down at his leg as he realised he was not using his cane, the one he had used since he was shot in his leg and crippled years ago. Smiling he looked up at Ronan and Zelenka as he realised the pain was gone.

"Good days and bad days. Alright, let's get to work. I want a complete search of the database of that Ancient ship… I'm, I'm feeling lucky today"

**In 2045...**

A cold and harsh wind blew over the snow-covered cemetery as the ground was frozen almost as if it did not want to accept the coffin, empty but for a single dress uniform and an old photograph of John Sheppard in his youth. While the coffin was carefully lowered into the ground, the twenty-one gun salute rang out in the freezing air while a large formation of aircraft flew overhead. Stood at the head of the open grave, President McKay spoke of his old friend as the coffin came to a rest.

"He was my commanding officer, my mentor and my more importantly, my friend. For those of you who knew him he was a great… pain in the ass, I can not tell you how many times he pissed me off with his…"

For a moment, he laughed as gasps came from those who had gathered around.

"… But he was more then that. John Sheppard was a great leader, he would put himself in a position where he would risk his own life to save another, and that was his greatest gift. I can still remember the first time I met him, I thought he was an asshole. Just a Helicopter pilot who got lucky with an ancient chair, but after the death of our military commander on Atlantis, he took over… I admired him; he taught me everything I know about the military. Not that it wasn't much I didn't know…"

Once again he laughed as memories flooded back too him.

"On more then one occasion I called him, I called him Captain Kirk, because he had a way with… alien women, something I also admired let me tell you"

Out of the corner of his eye, he saw a figure stood leaning against a tree. Although it was nothing unusual since many had gathered, the clothes of the figure stood out too him. It was a male figure, roughly early 30's wearing black trousers, black shirt open at the collar and black sunglasses. Smiling too himself, he thought it must be the son of John Sheppard as it looked the right age and almost identical to the man he once knew in his youth.

"But the reason we are all here is to say good-bye to an old friend…"

From the corner of his eye, a second figure appeared, a female roughly the same age. Yet, in an instant, he recognised the face; his jaw almost dropped as the two nodded slightly and disappeared behind the tree. For a moment he stopped, as he looked at the tree, expecting them both to appear the other side, nothing, they had vanished from sight. Smiling too himself he looked back at the open grave as the gathered guests looked at him as if waiting his next words.

"… Goodbye John Sheppard, my old friend"

Once more, a twenty-one gun salute rang out as the President saluted the open grave and finally walked away. As the crowd dispersed, Ronan walked towards the President with a slight smile on his face as he spoke.

"You saw them, didn't you?"

"I don't know what you mean" He smiled.

"Near the tree, you saw them, both of them"

Smiling slightly Rodney grabbed his old friend and pulled him close for a slight hug as he whispered.

"I did, John and Jennifer. Maybe there is hope after all"

* * *

_After the Great Tau'ri War ended, Lieutenant Colonel McKay left the Military and remained on Atlantis as a civilian advisor. In 2030, McKay was elected President of the Tau'ri, serving an unprecedented three terms in office. In 2046, he resigned the Presidency and lived out his remaining years in the Great City he given most of his life to until his death at the age of 102 years old, surrounded by his friends and family._

_He never reached ascension._

_General Ronan Dex served two more years as Commander of Atlantis, until he disappeared from history in 2047._

_Jennifer McKay, daughter of Rodney and Karen McKay remained on Atlantis as Chief Medical Officer and eventually left Atlantis, she was never heard from again._

_Samantha McKay married and lived a long life with three children and her husband on Langara after her Husband took up position as Commander of the Third Fleet based at Langara._

_Karen McKay, Wife of Rodney McKay, Died in 2056._

_The Tau'ri formed 'The Second Great Alliance' along with the Tok'Ra, Jaffa, Langaran people and eventually a species known as 'The Nox' _

_In 2016, a major rebuild of Atlantis had begun, larger and more powerful then its original design. Every city on Earth had also rebuilt, yet in the image of the new design of Atlantis after all technology was publicly announced in 2046._

_After the resignation of President M.R. McKay, the presidential race was won by Rya'c and J. Sheppard Jr by a landslide victory of 92%, eventually becoming the only Presidential team in history to take four consecutive terms in office, with a career spanning twenty years._

_Although it was still classified what happened to John Sheppard and Jennifer 'Jenna' Cole, Some people say they ascended, most speculate they will one day return to mortal form when Earth and the Tau'ri need them the most._

_Known as guardians of the knowledge of the Ancients and the Asguard, Earth and the Tau'ri would never be challenged again._

_The End._

_Story By_

_Ariston 1_


End file.
